Thanks Valter for all your help! I finally got the whole thing installed, and it sounds great except for the alternator whine.
I need help on elimanating the noise.
I ran the RCA cables down the middle, the power wire down the middle of the passenger's side. All the speaker wires acorss the back and up the sides, but they do come close to the ground wire. Will the ground wire make it whine?
I tried to do some research on capacitors but I dont know where or how to connect them.

Thanks again....

 

In most cases alt whine caused by poor ground of headunit and/or amps. Check all grounds. It's better to connect headunit ground wire directly to bare metal, then to factory ground wire. Try disconnecting radio antenna from HU. Gains set correctly? Also, please check out this post, very informative:
http://www.caraudio.com/forum/showthread.php?t=198477
Disregard any Pioneer bashings, they are awesome headunits
Also, here is a good page:
http://www.termpro.com/articles/noise.html

 

Its amazing how a small item can correct a huge issue.

Thanks valter for all your insite, suggestions and help.

Jack..