I am sorry to hear you are having so much TT/Empeg trouble. I have a very similar setup to what you describe. I have a 2001 TT roadster w/Bose. The only difference is the roadster has a subwoofer. Unfortunatly I dont have any anwsers, only some info on what I did.

I had to fabricate an interface to continue to use the bose amps - I couldn’t find one for sale here in the states. The setup is documented HERE

As you can see here in the wire diagram :


I had to do all 4 channels. See my post in the installation forum describing my issues with the rear channels (or anything less than all 4)HERE.
I would agree that if you hook up only two channels you would get sound from the rear. Its also true is you only hook up one (say the left front), you will get some amount sound from each speaker (but loudest at left front). I think this is because of the effect processing. I think there is some delay, or stereo enhancing going on in there.

I have not had to make any special EQ settings to compensate for these bose oddities. I run the loudness between 5-6.5, and tweak the treble (hi-jack feature) up +1. I am running ver 2.0 with no problems in the rear speakers.

If you have further questions feel free to email or IM me. Good luck