Cool I'll give it a whirl. So you could go wipe out the bad guys then start missions, or do they just respawn?
I used to go around sniping most of the guys I could before I did a mission.
Get all the towers you can be bothered to get at first as this will give you new guns. Once you start to take out outposts it gets a little boring as everywhere is full of your guys with no random pirates to kill.