Hopefully anyone who has managed to beat EG can help me with this, as every time I play it I get to one point that forces me to give up. Around the time that soldiers start appearing. Basically that shoot up all my minions and even with red alert sounded my minions just run one at a time and get blasted. I tried using the minion gather from my henchmen and that still doesn't work. Has anyone found an easy way to deal with them that doesn't wipe out their entire minion pool?

Set traps and lure people into them to eliminate some. It seems to be a game of cat and mouse where you are the mouse trying to outsmart the cat!

Sub-Actuality gave some excellent advice.
In addition to that it is important to have a good layout of the (one!) entrance area (at least on the first island). I always put a huge training area right behind the "maze" with the traps. Then I wired the cameras of the trap area with the speakers in the training area. This way some of my best guards (the teachers!) would be at hand to deal with intruders without disturbing the rest of the base.
Another possibility is to place a door to nowhere in the entrance area of your base. Then put it on **** 4star security. NO ONE will pass this door to nowhere and two of your henchmen will guard it, and the hallway it is in, at all times! But make sure there is at least one space to the left and right of it (for the guards) in the hallway.
Generally it is a good idea to kill people only when it is absolutely necessary. The hotel complex is a bit expensive but quite worth it in the long run. Otherwise you get in a spiral of heat-generation and there won't be enough space for bodybags in your freezer!

I did have Jubei as my main hench and the same thing happens, he warps into the group and gets taken down fast. Usually an exceptional group of soldiers spell doom for me.
My last game I was playing as Max with Jubei ,neurocide (not a smart choice it seems) and the big Aztec guy
I didn't know that cameras and the tagging system were supposed to be used in tandem and never really used the kill tag until they were in my base.
For my base I do focus on military and science minions but I kept rooms like the training and armory further inward. So far my best run at EG was to the second island but never got farther then that.

Actually there are only two islands in the game. You will spend a LOT more time on the second island than you did on the first, though. Anyway, it sounds like setting up an efficient security network will really make a big difference in your survivability. If all else fails, you could try playing on a lower difficulty (if it's not already on Easy).

The advice offered will be a real help, but if your interested, there is a whole site dedicated to the game which contains loads of guides. For a specific level-to-level walk-through, consult this list here. But I'd only use this if you're really stuck and you're pulling your hair out!

In addition, search youtube.com for some advice on setting up false entrance and trap entrance areas.
I build lots of camo guns outside with overlapping fields of fire. Seems to work well. About the only problem I have is when Super-Agents get ahold of my defenses, they take them down quick. You have to tag SA's fast to debuf them, to keep them from doing anything.

On my first play through i relied on social minions to take care of intruders, I had practically no traps and used Jubei to take care of anyone who wandered too far into my base!
Worked quite well i must say :)

Here are some tips that served me really well:
The most important thing is to build your base like a evil genius!
You could of course build a normal base and kill everyone who tries to enter, but thats just evil and hardly genius, so listen up my little evil geniuses in training.. this is how its done!
Build your base in a fashion where it looks like a normal company ( that is tasteful enough to put their HQ on a volcanic island of course. ).
This means, avoid putting any heat generating items near the entrance.
I suggest the following:
Make one base entrance, 1 star, completely open.
Inside a corridor which goes to your sleeping quarters with a 2 star door
Put a whole buncha bunk beds in there, and a door on security level 3, in the space behind the door, put a whole bunch of lockers only.
On the other end of the corridor that lead to the sleeping quarters, put standard things such as a mess hall and other default non heat generating things.
Then put your evil base buildings at the end of those legit buildings.
This setup will help a ton. Agents will land on your island, enter your base, see the locked door to the sleeping quarters, enter it.. see the high security door, and try desperately to break in. But as long as they don't find anything incriminating, they will leave which actually LOWERS your heat rating ( investigation revealed nothig suspicious after all ).
Additionally, put a whole lot of topside shacks up, put sleeping quarters in them with some lockers, and a 3 star security door. Agents will waste a lot of time breaking into them just to find 2 smelly lockers. =)
Speaking of lockers, always keep enough to have the maximum quantity of minions. I also recommend putting the control room in a much frequented area, then put your evil genius in there, so he constantly gives bonus benefits to the people working in the control room. Occasional executions help as well.
Make sure to keep artifacts / rare theft items hidden away safely in the illegal part of your base.
Also make sure to abuse the cloning vats liberally. A cloned evil genius that gets killed lowers the pesky attention you receive by quite a bit =)
And of course ..don't forget about a trap filled tunnel with a security 3* door enclosing it, to laugh manically at curious agents ( not really effective, nor needed but fun !! )