I believe that presence channels on the yamaha recievers are optionally used instead of surround backs, above the right and left front channels... a zone 2 would be or a diferent room. in response to your post about how to hook up the sub, unless i missed someone else's reply, is that that sub was created before/to go with a reciever that had no lfe output, so. a person would get a set or rca's and come from the left and right front channels, to the input 2's or route your front speaker wires through the in and outs of the sub, before they go to the speakers. this way you can't control the crossover and level from the reciever, but if you are just runing your lfe output to the sub, you definitely arn' tgetting what the sub can do.
in other news... did you say you were hooking another sub up in the other corner of the room? What did you end up getting?
good luck!
-Parker.