just for you to know...I didn't like the sound of the stock head unit, so what I did was install a Rockford Fosgate 3sixty.2 processor. This allows the stock outputs to be into it, and then "fixed" so they are flat. Additional adjustments include 31 band EQ front, 27 band EQ rear (not that you'll use it), 15 band EQ sub, and full time alignment. It is all controlled using a Palm Pilot or other similar product shown to be supporting on their main website. From the processor, you hook up your amplifier(s) via RCA out. The results...to say the least, were astounding. The stock front speakers actually sound GREAT stock, and with a subwoofer, it was wonderful. Naturally, there are improvements one could make to the front end speakers, but it would be one of the last things I'd do.
In order of importance:
Wiring (power, ground, RCA, fresh speaker wire)
Full sound deadening. I used Raamat, and Ensolite. I recommend the same. 50sq. ft. raamat, and 4 yards ensolite dead minimum, to do the car correctly.
Amplifier(s) based on what you want to use.
Quality subwoofer(s) immediately after the amp(s). I used the spare tire well to fiberglass a box. Tough stuff!
Advanced processor, or very high-capability head unit. I didn't want to lose the stock integration and design, so the processor was an easy choice for me.
Front components, or DIY (make your own) setup. Like SEAS, Dayton, Lotus, Vifa, etc. Or, go the easy route and run JBL GTi, Eclipse Sc's, Pioneer PRS high end, Peerless, Rainbow, etc...the list is infinite.
After the front components I'd consider the system DONE, but if you must do rears, go for it.