Unless you are shooting for a competition level system, I would suggest the following progression. Just stop when you're happy with the sound and you won't have to buy anything unnecessary. For the time being [ST]I've stopped after step 1[/ST]. [EDIT: I stopped after step 2.]
Step 1: Install some kind of sound insulation (Dynamat, Brown Bread, etc... They all do pretty much the same thing) in your trunk, front doors, rear doors, and under rear seat.
Step 2: Use
THIS and the quality mono amp of your choice to power your stock sub. You can fit all this stuff into your spare tire well along with the stock sub, like THIS. The amp powering your stock subs right now is downright pitiful, and is definitely the weak link in your low end.
I used THIS instead of the epicenter as I'm not really going for audiophile grade sound in the FX. It works perfectly and is a tremendous improvement over stock. (Be sure to size the amp with possible sub upgrades in mind. It's better to overpower than underpower subs. The real enemy of subs is distortion, not wattage.)
Step 3: Use the Cleansweep or equivalent and a quality multi-channel amp of your choice to power your stock speakers. (Be sure to size the amp with possible speaker upgrades in mind. It's better to overpower than underpower speakers. The real enemy of speakers is distortion, not wattage.)
Step 4: If you need more bass, upgrade your sub. There are many options to fit VERY capable subs in the spare tire well. My personal fav is HERE.
Step 5: If you want better quality mids/highs, upgrade your speakers.
If you make it past Step 5 and still aren't happy, then you'll need to start replacing the weakest link systematically until you're satisfied.
Good luck!