Interesting. Maybe you can daisy-chain the CD changer input through the empeg's aux-in port?

In the original installation, did it go like this?
Cd Changer-> Bus Audio In

If it did that, then maybe you can do this:
Cd Changer-> Empeg Aux In
and
Empeg Front Line Outs -> Bus Audio In.

If that works, you're golden. Just set the head-unit to "Cd changer", leave a CD in the changer, and use the Empeg to switch back and forth between Aux and MP3 Player.