When I declared independance I had recruited a lot of level 4 units. When it came to the defense of my colony most of them didn't show up, instead I had a lot oof the level 1 uinits from native allies, the colony itself and the forts, How can I field more level 4 units?

I think they have to be attached to a general.

Keep a decent general in the colony.

You may make specialist garrison commanders with at least 9-12 attacks and only about 10 units, defender get a bonus on number of units (not sure but about +4 or +6). Plus there the militia and cannons from forts, and native helpers (if you got friendly natives near). The number of units your leader can control still matters, you field more units if your garrison commander can control more, but NOT just all you have inside the colony. But as long he can control at least 9-10 units, the number of attacks is more important. And if there several generals inside your colony the one with most attacks takes command of defense (or maybe it some trade-off of number of attacks and number of units, but strongly in favor of attacks).

It is likely not relevant is the units actually attached to the general or not, or to what general are they attached as long they inside the colony.

Defending against Mother Country is actually quite easy usually...
They send just one attack at a time, and not every turn.

A human player or over-developed AI on hard difficulty settings can send multiple armies to hit in one turn and/or every turn.
And In that situation there is some quirk I can't really resolve yet, how to keep your damaged units from showing up in the next battle, sometimes I have 50+ units in a colony, most of them fresh, still I forced to defend with previously damaged units.

Between the turns you, of course, may use your transport generals to swap damaged units with fresh ones from another colony. Not sure, but the actual order of units in unit list may or may not help, you can try to modify that order by attaching/detaching units to generals inside the colony.

But, if you expect multiple attacks in single turn and have sufficient reinforcements available, it generally better to let your heavily damaged units die in first battle(s). It also wise to save your militia/natives and fort cannons for later, if they die in first battle, you don't have them in the next (in the same turn).

I love to have level 5 (strength 6) units, and always try to keep units alive whenever possible, but in high intensity war it is faster and safer to rebuild them than heal them.

Just some notes :)

The colony defense Unit Cap bonus is +6

It does not matter units are attached to a general or not - what matters is the order of units in unit list: first X units from the list will defend your colony (where X is Unit Cap of your best general inside that colony +6).

This order can be altered by attaching units to leaders inside the colony - the natural order is historical order of recruitment, but any container in unit list comes in place of oldest unit within that container. Leaders have they own natural place in the list themselves, and this is a good utility for your oldest leaders - once they older than any unit in given colony, any units attached to them come at the beginning of that list.

Therefore, I now usually assign the 6 "extra" units to an old leader (kept around just for this), and a desired mix to garrison commander who is pinned right next by including oldest unit (ideally, that will be an artillery piece, perhaps even a level 5 one). This way, anything that comes after does not really matter, at least for the first fight in the turn. Remember, if you have more than 6 units before your garrison leader, last units of your garrison leader sub-list (if it is full) will not show up.
To fully organize the whole list you may need two more leaders... and sometimes even accept presence of one wounded unit in your defense selection.

Worth to note, units heal before the first battle take place, so one-point wound can be counted as full force for defense purposes.

Also, units hired right on the eve of battle will show up (from the very end of the colony unit list, of course), but Leader don't - they are born outside the colony center and must enter it first (or be placed in via the full Unit List if colony is in hostile territory), what only is possible next turn.

If there multiple fights at the same turn, units wounded this turn are moved down the list (virtually)... a bit. Not sure about details here, but chances are you won't get them in second fight if have a support leader with fresh units parked right next to garrison leader in the unit list. With list left unsorted, there is fairly high chance you will see some, even if have 50+ units in the colony. So it worth to take a look on your battle-station assignments before an imminent attack.

If there is no leader in the colony, I believe you get a virtual one with default stats (like what could be hired from that colony, but with extra points undistributed).

A lot of useful tips here, thanks guys! What happens to your other armies garrisoned inside the city, if it falls to enemy hands? Let's say you have 3 armies, one gets wiped out. Will the attacking forces be forced to face my other armies or will they occupy the fallen city and slaughter my armies without a fight? Or will my excess armies get kicked out and will appear outside the city on the next turn.

This is yet to happen to me, but I'd like to be prepared. I've just started playing this incredible game on normal difficulty level. I've first encountered it in 1996, but it was only a demo and I didn't know English at the time, which made it very difficult to play it, but I was hooked regardless. Everything about this game is perfect, the atmospheric setting, the intro, the strategy, trade, city building. I even love the chess like battles. I don't mind the graphics at all, they hold up quite well considering the age of the game. After stumbling upon it on GOG - I knew that I just had to have it!

I've just won my war of independence, which was surprisingly easy, except for one battle when my smallest of colonies was attacked by both the mother country and an opposing AI (the sneaky bastard wasn't even at war with me) I was victorious nonetheless, but took heavy casualties.

This not really accurate.
Once inside the town it does not matter how exactly the units are organized in regard to attachment to generals. Re-read my previous post carefully, I discuss that.

I will chose to read it:
"if I have 3 times more units in town my best general can field in defense, and still I lose the fight..." Kicked out.

If you lose the actual battle colony change hands (or is totally wiped out in worst case, if that was a raid), other units not on the battlefield right now have no chance to get involved if you lose battle.
They are not killed or damaged, but kicked out of the town and appear on the map. In same cases you can use them to immediately retake the town next turn.

Overall it is of high importance to win defensive battle, regardless of cost.

Also, if your intend in offensive raid is mere robbery and you do not want actually raze enemy town (maybe to capture it with next attack, for example) it takes some experience to catch the right moment between maximizing damage and still retreating before AI does (and thus save town from total destruction).
I would love if there was setting somewhere to disable AI from retreating raid attacks.... :P

. Independence war is not the hardest fight you can face in this game, more, it usually is easily to predict and prepare.

There is bunch of parameters that influence size of Mother Country troops and number of attacks they launch, I can't recall all that right now, but I remember I read about that here in this forum also. That involves difficulty level, is Mother Country involved in wars on its own actually, possibly game turns passed, number of your colonies, etc, with some randomization on top.

As far I remember, Mother Country attack your first colony or smallest colony in first attack, and smallest colony with all follow up attacks.

By the way, losing colony to Mother Country is probably the least damaging lost battle possible, you can not only take it back, but also just win against one or more of its attacks to win the war and occupied colony will be returned to you intact.
All European players face independence war at some point, and AI lose colonies to Mother Country too sometimes.

Colony Defense:
In my experience two things happen when you lose a battle for your colony.
1. If all of your units are destroyed at the conclusion of the battle then you lose all the surplus units you were storing. That is why when I attack I do my best to destroy all the defending units.
2. If just one of your units escape then you get all the surplus units, expelled from your colony at the start of the next turn, that is if you have any. Sometimes you just end up losing them in the battle.

Leaderless Colonies:
If you have a colony without a leader you have a standard of three attacks. If you control Temples of War then, depending on who you play, you gain 26 additional attacks; even without a leader present.
If you control an ancient ruin sometimes you get free warriors ranging from four-five hit points. I have had to control several ancient ruins to get level five native warriors, and they are beast.


I have always understood that charisma and reputation are what allow a general to field additional troops in excess of their allotted amount when defending a colony. I am not sure if it depends on how may forts you have, but I could see that having something to do with it.

But always station generals along a known flight path so they can intercept, weaken or destroy incoming generals. Also have level Four boats out and about to attack seaborne threats.

Cheers

Hmm, have to test this, can be you are right. I mostly love my experienced commanders too much to allow them to die anyway (and that is what to happen if you kill off all your units in any fight), so I do my best to retreat when things get really bad.
A raid attack on large important colony might be exclusion where I would fight to last breath, but such not happens often if you are mindful of what you do. Sure, you get special bonuses regardless.
26 (!?) attacks without leader? My best guess is, you control multiple Temples and play as Native (then it 8 additional attacks per temple, as far I remember, so 3 Temples required). Maps with multiples of Temple and/or Ruins happens so rare you really have to generate dozens upon dozens in scenario editor to get that or be unbelievable lucky ;)
And it makes no sense, there is literally nothing to do with that much attacks (European player could use up to 27 in extreme case, Native don't have cannons so 18 attacks is all they ever could use) To be honest I not really understand either of those, but whatever the effects are they are so faint they surely not worth dumping points in anyway. I don't have recent tests with extreme values in either to refer to, but as far I see the command bonus in defense is flat 6 as far your own regular units are concerned.
In my best understanding:
- Charisma influences how many native helpers you can get, that is if you are in position eligible to any, and that all it does as far I see
- high Reputation will make AI enemies to retreat sooner, actually something I don't see as bonus at all in most cases. But can be helpful in town defense indeed. Forts control how many garrison units you have (those low level units with red numbers).
To have garrison cannons you need higher than first level forts (Lvl 2 if I remember right, maybe 3) and there one per fort (per level?), but only up to 3 total. In short, it max out at 3 high level forts (or possibly just one Lvl 4 already, don't remember right now), more will not give you any more.
Once present, the garrison units will be there regardless of leader, and they are regenerated for free each turn, however, if multiple fights per turn happen, and you lose your garrison units in first, they won't be present for next battle in the same town the same turn. True, even if you can't defeat the incoming force, you can use your fast leaders to slow attacker to a crawl with hit and run tactics, each successful intercept cost them a turn even if you retreat right away. That way you can prevent multiple attacks one turn and/or give you time to get ready. It is also crucial to intercept attacks that could be raids outside.
However, it often beneficial to take the risk and let the general battle to happen in town defense, the extra units defense gives can very much decide the fight (assuming you have those extra to field of course).

Excellent Points...

I WROTE AN ERROR

I believe when I was writing that post I must have accidentally highlighted and deleted some of what I was writing. Pesky laptop touchpads!! Lesson, proofread.
At the time I wrote said post I was playing a game as natives. I had three temples of war giving me 27 not 26 attacks (default plus 3included) in an leaderless colony.

NOTE
If you're the natives and you attack a european colony that is controlled by its mother country you get to keep that colony. If it has any level fort, let alone level four, my dear lord, boom boom sticks galore. You can build canons and add them to your armies. That is when 27 attacks coupled with natives canons and their attack bonus make mincemeat of your enemy. And their canons, though in desperate need of a new rendering are maybe, "overpowered." They look like a native general and when they fire, it is the load globe you see between turns.

As for Charisma and Reputation; I know they do effect combat. It plays into both attack and defense, coupled with your research. The attack plus I think goes without needing an explanation. But I will explain if requested. The defense plus gives your units staying power when they are hit, literally. It helps units stay in the square as they take hits and not run. I have experimented with generals of varying levels of each attribute. The lower you devote to said articles the worst off you are. As the AI itself researches, the natural result is death and mayhem for your front line with maybe one unit surviving with +1. You know when you are fighting an AI with high charisma and reputation because your attacks are not as havoc wreaking. And that is why you use the cheats. ;-)