Stereo opinions run rampant here as other places. There are a few guys who have very good and expensive equipment (AFBeefcake for one, off the top of my head - there's others). Trevor has some sort of background in audio and always seems willing to help if asked serious questions.
all that said, here's my opinion (for what that's worth) for the lazy man.
Get a decent pair of component speakers for the front (this has a heavy $$ dependence of course). lose the 6X9s in the back. do a search on how to pull them out. Put the grills back in but leave the holes open so you box in the trunk has a path for the sound to come through.
Need an amp for all this of course, with crossovers properly set between components and subs.
if you want to read about some basic facts first, try this site:
http://www.eatel.net/~amptech/elecdisc/caraudio.htm