The rule of thumb is that the stronger side (the side trying to win) should put the pawns on the opposite color of his or her bishop (so that they don't get in the way), and the weaker side should put pawns on the same color as their bishop in order to defend them an extra time (defended with the bishop and the king, the opponent can never win a pawn).
There are obviously exceptions to this, though. Each position really has to be judged independently.
One key idea, however, is that it is usually a good idea to block your opponent's pawns on the same color as the bishops (assuming that the two bishops are both light squared bishops or both dark squared bishops). This gives you the chance to try and win the pawn later and it will restrict the movement of your opponent's bishop.
If you have the only bishop on the board (your opponent has a knight, for example) it is almost always correct to put the pawns on the opposite colored squares of the bishop. This is usually the only way to play for a win. This touches on the good bishop/bad bishop question, but if your bishop is bad, then the knight will many times have the edge. If your bishop is good, however, you can try to make use of the bishop's superior range.