Personally, I like my skull-boys to be exactly the kind of terrifying military machine the setting makes them out to be. Sure, your group can burn down a squad or two when you catch them off-guard, a rifts group is often powerful enough for that, but when they take cover and call in the artillery and air strikes...things get @#$*()% ugly.
![Twisted Evil :twisted:](./images/smilies/icon_twisted.gif)
From time to time i'll have their seek and destroy units or long-range patrols out in areas that aren't CS controlled, sky cycles will do fly-overs of suspect areas and the such. Though I don't have platoons of UAR's wandering the countryside just waiting to get blindsided by the next group of murder hobos that spot them. The important part of this is that a high altitude SAMAS patrol won't automatically engage everything it sees. They'll often just spot you, report what they see and more often than not command won't order them to frag you unless you're steering toward their territory. Even then, they'll probably just warn you off over the louspeaker.
I also tend to keep them focused on their goal. They have their armies deployed in areas they want to occupy, then patrol the rest. they kill a lot of stuff, and much of it is unnecessarily tragic, but they hardly go out of their way to torch orphaned d-bees just because they're there...unless they're annexing the area.
Though there are times i'll have a comically tragic CS officer and his men take a grudge against the PC's somewhere over the rainbow...that tends to be entertaining.