stereo/cd player

Only if you have one of the Mach audio systems. It's the way the amps work as far as I know. If you're running the base system of 4 speakers and the radio itself you shouldn't have a problem. But remember an aftermarket radio will push your factory speakers (if you still have them installed) hard, and might blow them.

I myself have a pioneer cd player and speakers and everything works just fine. the speakers are even wired into the factory speaker wires.

You can't really see it but i simply cut the factory connectors and crimped the speakers onto the wires
http://photobucket.com/albums/a108/AndyG47/?action=view&current=rear9.jpg

Install help

Changing over to an after market is not a big deal, with or with out upgraded factory amps. Metra co. makes wiring harnesses for either application. If you go with a high power after market unit you want an "amp by-pass" harness. Just call Metra tech support they are great. They have a
good web site, but they don't list everything they sell. That is why I always call them and tell them what I want to do, and they tell me what is needed. Also, changing just the front door speakers will make a huge difference.