From what I have found, the stock amplifier should not be used with an aftermarket head unit. The factory amplifiers have internal crossovers and cap points to curve the music... not what you want to have if you are upgrading your system.
If you are an electrical wiz, you may be able to rig the changer in to the aftermarket head unit... and it may be a straight plug in with an alpine unit. It's hard to say until you go and compare plugs, and even then it may not be a direct fit.
I'm going to attempt to bypass the amp, use the factory head unit and changer, and run my own amping system/sub/speakers. I've got all the pin-out diagrams, but it is still a big pain in the arse.
There are several companies out there now making adapter harnesses to be able to run your factory changer with an aftermarket head. Check with these guys... they may have the one you are looking for:
http://www.installer.com/wires/index.html