I handle IC in a program exactly like physical guards on patrol. You can hide from them (with the Stealth program) and they use perception (Pilot + Analyze) try and find you. If they find you, then there's cybercombat or alerts or hackers or whatever, that parts up to you. I think what you're asking, though, is how many IC to put on a system? Again, that's up to you. I don't limit my hosts to a System rating of 6 especially for larger corps, for example, while you may want to do so. But, as you say, you can run IC programs to roughly (System x 2)-1 usually without too much of a problem, which can provide for a small army running around in a host if you need it.
As for your PCs starting with one Agent program and an Attack program and spawning small armies of their own, I don't see why that would be a problem. Clearly, if they run too many programs then their system will suffer which will also effect their initiative and the initiative of their brood. Just remember to load up that zergling icon when you pull this trick

'Course, when you dump that brood onto a host, that host could be running Analyze on itself to detect increases or decreases in its responsiveness and might start alerting hackers that something strange is going on if you pull this one too often.
As an aside, I often state that if you screw up the software duplication, you destroy the software from which you're duplicating. Not that bad for common-use programs but this house rule has kept my gamers from pirating some of the higher-rating hacking and agent programs that were purchased at character generation.