I never had a CD-Changer, but yeah the computer is hooked directly into the amp now for audio. An FM-Tuner card provides the radio and the CD/DVD drive in the overhead console serves as a CD-Player. The amps come on with the car but I have a switch where I can manually turn them off when I need to
With enough work you could have a car-pc control an OEM BMW CD-Changer.. all you have to do is send the changer the right commands v ia I-Bus and hook its audio output to your line-in. You can work backwards from the CD-Changer Emulation code on the HackTheIbus Yahoo group.