Attached is a rough diagram of the way my 2 HUs are wired up (I'm sure I missed a couple of the wires in there, but you get the idea).

Ah, OK. You're doing a standard daisy-chain, using the empeg's aux input.

The first problem I see with this is that you're connecting the head unit's "amp out" directly to the empeg's "aux in". If my guess is correct, those wires coming out of the head unit are not line-level, and could overdrive or even damage the empeg's aux-in. They are somewhat amplified already, if I remember the way these Bose systems work.

Are you saying that you hooked it up that way already and it worked?