OP, you can get an MTX re-q to make your factory signal pristine. it will also allow you to use amplifiers with low level inputs for better sound quality. oh, and it gives you a specific subwoofer output set for use with a sub amp. super easy to hookup, you just tap into your stock speaker wires to get the signal.
they have things called 'line out converters' that are basic version of the re-q, but they don't restore the signal like the re-q. your radio as far as i know offers a signal that has significantly reduced dynamics, in order to reduce distortion with the lame factory speakers.
if i were you...
i'd get the re-q (does your car have tweeters in the sail panels inside where the mirrors are? just curious) anyway, i'd get either a good set of 6.5" coaxial speakers like the alpine type r set or something like the alpine type r component set that has both the tweeters seperate from the woofers. These require more installation work though. the coaxials might be just fine for you.
then i'd get a nice 4 channel amp, use the front two channels for your front speakers, leave the rear speakers stock and powered by the stock head unit, and then bridge the rear two channels of the amp to power one 8" woofer in a nice, properly designed ported box. the boxes they sell premade will not work; you should spend the money to have someone either build you one based off of your woofer and a program, or possibly have someone walk you through designing the box with a program like winisd and you build the box yourself. depends on how adventurous you are.
so, 'big' parts list is-
mtx re-q
front speaker set
4 channel amp
8" sub in a ported box
small parts would be stuff like patch cables, wire, amp wiring accessories, etc.
the hardest part would be running the speaker wire from the amp to the speakers in the front doors, but it's not THAT difficult.
i have a very similar setup in my car. i've posted a few pics of where i installed my amp and re-q, etc. i didn't need the re-q because my bose signal is nice and flat, but i wanted it anyway because of it's flexibility. i also am running a big sub in a huge box, but it's a personal preference. i'd probably be happy with an 8" woofer, i just overdid it.