Mud slut, first I want to say amping your door speakers, basically adding an amplifier to them instead of just the aftermarket HU will be equivalent to the jump going from stocker (HU and speakers) to the aftermarket HU and speakers, DO IT!!
As for the subwoofer you have 3 locations to choose from, and 90% of your sub selection will be limited to shallow mounts.
Behind the seat, shallow only, or very few conventional subs, usually 8's or some "shallower" 10's check out
www.spl2k.com for some examples. If you have a power sliding rear window this will greatly limit your volume.
Under the rear seat, this will be more of a custom build, I know JL audio makes a stealth box for this location, and some audio shops have also made boxes for here, but I don't know of any readily available boxes for this spot except from JL. Mikey ran a box in this location that a local shop built for him.
Center console, sounds like you have a 40/20/40 setup, for this you can purchase a JL stealth box, build your own stealth box (907Dave built an awesome box for himself in this location,
http://powerstrokenation.com/forums/showthread.php?t=75756&highlight=dave ) OR if you are interested in ditching the center jump seat for a 08 center console, you can easily fit a conventional sub up to 12-13" in the center console while still maintaining a good amount of storage space.
Once you narrow down a location, then the available air space and mounting depth will dictate your subwoofer selection, then with a sub selected choose and amplifier that will properly feed that sub. Budget will be the next primary factor for all your selections.
As for boxes/subs/music selection, all subs can be made to sound good for all music, it just takes some time and careful tuning of the box. Basically a sealed box is the easiest for tuning and also to squeeze into these trucks, but the trade off is less overall output, where a ported box will have the highest overall output but can be a challenge to tune properly for the sub and the cabin.
Yea I know you need a certain amount of volume for the sub to work to it's full potential, I just questioned it cuz my 12's each came in their own pre-made box an they're alot smaller. I'd say they're roughly 15"x15" an maybe 6-8" deep. I thought they were a little on the small side, but since they came from the manufacturer that way I ASSumed they were good to go. When I do build my own box it'll be considerably bigger
He mentioned that his sub is in a ported box, generally ported boxes run double the size as their sealed counterparts.
