My A4 w/bose "premium" option has an external amp in the trunk behind one of the side panels. It powers all four speakers and the teeny tiny sub that came with the car. The stock option (non-bose) has a lower power external amp to power the rear speakers and sub, while the fronts are powered off the head unit.

Having the amp in the trunk was nice because I was able to tap into the line-level inputs and make RCA jacks to feed the sub that I just installed. The only wire I had to run was power (and I didn't even remove any panels to run that).