I'm not familiar with the larger Audis, but AFAIK Audi do a couple of head units, the 1*DIN Concert, and the 2*DIN Symphony, Replacing them may mean losing a few features like the dashboard display of radio/CD track & speed sensitive volume control. I'm not sure how easy it is to integrate the Empeg with the Bose soundsystem, which includes some amplification. I have the same problem looming, as my Audi S3 arrives at the end of this month.
Take a look at the forums on www.audiworld.com, a lot of the guys there have fitted after-market ICE systems to their Audis.

Philb.