Cool man. Well I myself am running two 12" Kicker CVR's and I will tell you from experience, it is really hard to fit in two 12"s in a ported enclosure, which if you are looking for SPL, you'd want to go with. I JUST finished the install of mine tonight and what I had to do was go with two single 12" vented boxes, and set them up so that at a later date, I can make a faceplate so that everything looks custom. If you don't want to go that route, you could do a custom fiberglass wheel well box, or just a straight up fiberglass box to take up your trunk. I was running a sealed box before, but I'm liking the vented better as it's a deeper base which works well for what I listen to. So as far as the subs go, I have worked with Kicker subs for awhile now and the CVR's are alot of bang for your buck. As far as an amp goes, you need something that runs atleast 800 watts at two ohms. I'm running a Kicker ZX750.1 which actually is rated over 900 watts and it hits hard. I know exactly what you mean by feeling it more in the seats and as long as you go ported, you will feel these not only in the seats but in your face. There are other options to go with for amps obviously, but it depends on if you want to do electrical upgrades on your car or not. That you will have to let me know.
For deadening, although Dynamat works well, it's really expensive. Even that trunk kit on Cardomain is really expensive as it only gives you 20sf which isn't enough to do most trunks, especially more than one layer. Now with my install I finished tonight, I put eDead in my trunk which worked very well. The best part is is you can get it for really cheap on eBay. I got 60sf of it for $50. I did two layers on my trunk lid and on that rear panel that my rear speakers sit on and I still have a full roll.
But anyways, if you want to go into this in more detail, let me know. We can talk on msn or aim or something, just give me a shout.