This is basically OFP's
Abandoned Armies that you're describing, except there're two sides and you get lead a resistance group. The spiritual successor of AA is
Punishment Battallion by Lee Hunt, which you might very much want to check out.
As to making it yourself, D.murphy man there has given you a pretty good starting point with DAC, although it can be a bit challenging for a scripting novice to get their heads around it (nice tutorials come with it though!).
However, you probably need something more than just SF action behind enemy lines ambushing convoys and blowing up buildings: but as it were, this is more of a
Mission Discussion kind of topic when it comes to actual content. You could start a separate topic there if you want to discuss those aspects more in detail.
As to questions:
Fuel: Not AFAIK, no. However you can refill the fuel tanks yourself with the setFuel command (look it up in the comref).
Units: More units will cause more latency, but ArmA is also streaming, meaning units outside of your visual range won't have as high an impact on performance as those right next to you. Nonetheless, it's always a good idea to use some kind of spawning/despawning script (which DAC comes with by default) for really big missions.
Your last question I don't quite understand: you mean if the player (for instance) kills a unit which belongs to a certain group/is in a certain area, then the player is given a new waypoint? It's a bit complicated, so I suggest you read the section on triggers and waypoints in the
Beginner's Tutorial to get a better understanding of how things could work out.
Good luck!
Wolfrug out.