I grew up in a Protestant church where the choir loft was always behind the pulpit, just like Buster29 mentioned. We also had a church loft on the opposite side of the room, but it was mostly used for overflow seating.
A friend of mine invited me to a Catholic Christmas mass, and I was surprised to hear choir music coming from the back. Their choir loft was almost completely out of sight in the upper loft. I could hear the music just fine, but I couldn't see any of the people singing or playing it. I guess that was the point, since the choir was supposed to suggest the presence of angels during the service.