I'm running an AoR campaign where the PC's are SpecOps rebel regulars and I was curious if anyone else runs such a campaign and do you cover pay for the characters?

I generally give them reasonable pocket change for small buys. If they want to buy something bigger we generally make a deal so we don't have to track money. I just make it something they can work toward and that creates some interesting story, like if they want a new weapon they have to record XX amount of Duty and then they can get it.

For starship combat, may be I've missed it, but is there some mechanic for accounting for the pilots skill in the difficulty to hit? or is it always flat & determined by relative silhouette?

Difficulty is flat, pilot skill figures in from ranks in Gunnery or whatever skill is being used.