Thus, my question is: If i get a bounty in a hold that was controlled by the Empire, will the bounty still be there after i eventually gain control of it with my stormcloaks?
Really, the game should automatically give you bounties in those Holds that are now your enemies of once you start the civil war. The game is too forgiving on so many levels, and it would be so much more interesting if it was like this. However, in correcting this problem, i don't want to get punished in the end by having to pay a bounty to my allies for acts of war on our enemies.