I re-did my entire audio system 3 years ago. I just wired the new head unit with the old wiring, which allows you to run the rear speakers off the stock amp. as for the fronts, I have the 4.25 pioneer speakers and they work very well. i have infinity 6x9 in the back wired directly to the stock amp. it is pretty straight forward it just takes a few hours to get it all set up.
Sorry if I am being to vague, if you have any specific questions I will try to help you out.