If I read you correctly (apologies if not) you wired the outputs from your HU and empeg together (in a Y fashion, where the bottom of the Y goes to car harness and the tops to the HU and empeg). From your description it sounds as if the wires in the harness labeled "Speaker" actually connect to your amps inputs. Is that correct?

I don't ever consider it a good idea to wire outputs together - what if one of them wants to be at 0V and the other at 12V? Easy to lets the expensive smoke out in scenarios like this... If I've understood correctly, you could solve this "properly" with an RCA-switch (I think a Sony model number has been posted earlier to the board - and is probably mentioned in the FAQ).

As to your setup, as long as you never have both units on at the same time you're probably OK.

/Michael