I purchased this game, as the concept sounded intersesting, and it was a style I had not played before, but I am struggling a bit going into it. The tutorial was a bit short, and when I got to the hideout, I could have used some more help, especially around the map, timing, timing of missions, and things like that. Is there a good document or maybe a youtube out there that goes into this a bit in depth, so I can get a sense of what I should be doing, how critical the map is, along with the pause and arrow buttons, perks and other related items?
Note: I have not started the second mission, as I am trying to get a better feel for the game.
There's a manual for it, which should be available to download from the "extras" section. It's probably not in-depth enough for what you want though.
You can check the forums here - a number of the more common issues that people have with some of the game mechanics are likely already covered in here somewhere.
If you have any specific questions that are not already covered, feel free to post here with more details - someone's bound to help. It's been quite some time since I last played this, so not sure how much I remember.
Some basic tips I guess would include always travelling with at least two agents, so you don't get ambushed - if they find a mission at their destination (those flashing red dots sometimes turn up missions, but not always), then you'll need two agents if you want to "scout" the mission map. Scouting is really useful, most missions will allow you to do it (if you have time - which is why I suggest sending two agents so they're already available when you get there), and scouting opens up two things which are really useful for tactical missions: support (e.g. surveillance initially, later you can get smoke, mortars, snipers), and the ability to have one (or more, later on) agents start the mission already on the map in disguise.
Most other possible missions you can put agents on (apart from story missions, scout and of course tactical missions) are generally useless - although later on when the number of missions increases, you may want to disrupt the enemy without doing a tactical mission just to save time (tactical missions award far, far more XP, plus loot and intel if done properly though).
There's usually no need to rush story missions, provided you don't have a "doomsday timer" yet - and even when you do get one, you have plenty of time, plus it's easy enough to just find and stop all the missions that increase it while you do other stuff. So if you want to get a feel for the game, and possibly pick up some more XP and better loot while you're at it - feel free to go nuts by exploring those flashing red pips and doing tactical missions.
Incidentally, you'll want to ensure you take down any "scouts" that may potentially increase the "danger level" before they complete their mission - it should tell you this somewhere on the map. That saves having to move bases too often. Speaking of moving bases, it's a good idea to keep some cash in reserve to cover the cost of moving (you'll see the cost once you start uncovering potential new base locations) - just in case your danger goes into the red, so you can bug out before getting raided (those raids, strangely enough, do NOT give you a tactical mission - you just instantly lose a bunch of agents and cash - so avoid those if possible).
Apart from that, try to ensure you escape before the timer runs out so your danger level doesn't go up, and generally try to do things stealthily so your agents don't get heat (although if they do get heat, it's really easy to get rid of it by changing IDs - it's not that expensive, and they're always teleported back to base so if they're at less than full heat, just put them to work on stuff at base till it goes down).
Most importantly, don't worry too much - even on the hardest setting, the game is very forgiving on the strategic layer. The tactical layer can be more challenging when you're starting out, but you'll likely figure out good tactics pretty quickly (you've likely already seen the ability to assault rooms - that can be very useful). Once you start getting better weapons - and especially silencers, so you can actually complete entire missions without going "loud" - the game becomes a lot easier. It got to the point I started restricting myself to only bringing in the larger/heavier weapons if they were also wearing "hostile" armour, just to keep some challenge in the game.