Please Help with Wiring Question

Hey! I'm not new to wiring stereos or electrical stuff, but I do have a question regarding my cd player. I am looking at getting a pioneer cd player for my car. My MACH 460 doesn't like burned cd's at all, and thats all I have. It gets annoying having to fast forward all of them like a tape player. My questions are.
1. What wiring is needed to install a new deck? There are two H/U's Tape/CD
2. Do I need to run new wire from the deck to the speakers or amps?
3. What do I get to fill the bottom, where the cd player is now?

I'm sure I have more questions but I'm in a hurry this morning.

Lemme know guys

Andy

I went to a ton of different places looking for stereos. I either want to get the sony explod with the black face plate that moves. Or a pioneer deh6600.
I was about to buy one, but then asked him what adapter/harness I need for my car with the mach460. He said that its going to cost me about 70 bucks for something to bypass the amps and 50 to install that. I read on here that you can just get a harness and plug it right in, and play it like stock, with all the stock stuff working etc. Speakers amps etc.

Can someone give me a part number and brand of the harness/adapter they used to be able to keep the mach460 amps and speakers working. I dont want to pay for that 70 piece of crap and no way am i gonna let them install it.

I'm about to say screw it and just run new speaker wire to everything

I bought FDK10 and FAI-3A, both from SCOSCHE and it makes no sense at all. The connectors for the wires dont fit on anything I've pulled out of the factory head units.