Hi jdilley,
There are general guidelines. If you have only one Bishop try to keep it on the oppositve colour of square from your most dominant pawn chain. Where you have two Bishops this isn't possible so try to move your 'bad Bishop' to a place where it is either free of the pawn chain or 'behind the scenes' strengthening the pawns in general. Have you tried to fianchetto your Bishops before?
It's often good practise to try to trade your 'bad Bishop' for a minor piece of the opponent which is better poised to play than your 'bad Bishop'. This gives you an advantage because you are removing a weakly positioned piece of yours by trading it off for a stronger positioned piece of the opponent. In some cases strong players will even trade Rooks for Bishops or Knights for purely positional reasons as, believe it or not, sometimes enemy Bishops or Knights are actually causing more trouble than your Rooks are causing the enemy for purely positional reasons and it's a worthwhile trade.
Hope this helps! 
I've noticed that overall I find my usage of bishops to be the clumsiest of all my pieces. Specifically, I have massive brain cramps at times regarding how to develop them. When the time comes to clear them off the back rank and give them new homes, I never know the best move. Does anyone have any ideas or hints? I know it's purely situational, but are there any general guidelines?