Usually it's better to get the speakers first, or at least pick and plan on what you are gonna get before buying an amp. Why? Different speakers have different constant flow ratings (RMS) and it would really suck to go and get an amp that is great for your stock speakers but is lacking for your new upgrades.
About installing a sub. You don't need a sub to get good/decent bass output. Audiobahn has some very nice 6.5" and 5.25" mid-bass drivers (under the mid-ranges and drivers section, not full-range or components). They come in a pair and depending on where you get yours they can run for about $60-120 (for the pair). They are 200watt RMS per pair so get a 2 channel amp that can put out 100 watts at 4ohms RMS, easy to find for around $100 at
www.cardiscountstereos.com or
www.etronics.com or
www.ikesound.com ...this combined with nice speakers should provide an almost complete range of sound.
I would use 1/2" MDFB to make some small sealed enclosures for the mini-bass drivers. They can be easily fabricated to fit under your rear bench seats on either side on the floor. Also, to hide and store your amps you could bolt and mount them to the tops of the enclosures. I think a decent set of speakers, front and back, mini-bass drivers, 2 amps, an amp kit and distributor/wires, and MDFB would cost around $500-$550. The speakers and drivers will run around $200 or so with shipping, the amps will run about $250 or so, an amp kit with a distributor and wires shouldn't run more than $100, and MDFB will run you $10-15.
Only thing with adding more than the door speakers is, you will more than likely need a new HU.
Another option would be to slightly alter/shave the mounting holes for your door speakers to fit a 6.5" speaker/driver. It's not hard to do since the existing holes are nearly the same, and some Dynamat Extreme can easily cover the gaps along the sides. A better approach for this would be to go and get the same sized MDF as listed above and cut out a new mounting area as it may be needed to fit the new magnet and voice coils. This route would run about $200-$250.
Good luck.
(I based my prices off of the 3 sites I listed)
Edit- Using Dynamat to fill the hole should only be temporary if you do that b/c it will absorb some of the resonance from the speaker. Not much but you may not get the full sound.