The system ( ahem ) that came in my car was just lame and I upgraded everything. Everything that I've read, which was quite abit says the best starting point is ditch the cheap factory speakers. You have door subs so you may not need one in the trunk. I got some really good deals from -
http://www.sonicelectronix.com/.
Doing the work yourself is easy and only takes about an hour or less for each door. The rear deck speaker are the challange and you may not even need to swap them, they are usually only for fill in and the fronts are for the sound stage. I have the JL audio component speakers in the front doors/ a-pillar and they sound nice. A sub woofer in the trunk will give your music a lot more body with out being boomy, but that's a lot more work then swapping the door speakers. The Crutchfeild website has a lot of good info but you pay premium for their stuff if it's not on sale, but you get premium support.
Hope this helps a little, I spent quite a few hour and $$ on mine. If you decide to go with the deck speakers I have some pioneers ts-d6802 that I bought for the front then replaced them with the JL audio. You can have them for $20. Only had them in for 4 months and I don't drive my Boss much.