Other things being equal (eg. prices, seating capacity, etc), my general guide is -
If audience is seated along the long and narrow, use rear projection (narrower viewing angle than front);
If audience is seated wide relative to the stage, use front projection (for its wider viewing angle).
Another thing to consider is available space in your room. Rear projecting onto a 9' x 12' screen with a 1.2 fixed lens will require almost 14.5 feet of throw distance. That's 14.5 feet of space you can't put audience seating in.
When space is tight, using a front projection setup can make a huge difference.