I built a box in my 03 extended cab with one 10" firing down. I left about 2" between the box and the floor. Then mounted the amps on the driver's side. Sounds pretty good IMO.

 

in my opinoin, i would go ahead and do a shallow mount 12'' sub they are made to fit in smaller places. thats what i did i made a custom box for behind my seat (i have a 1988 chevy c/1500 regular cab long bed)for 2 12" shallow mount subs and they sound good and arn't to expensive. on the other hand if you only want a little bass then do a 10" sub. i would suggest if you do a 10" then get the pionner sub at wallmart for a cheep sub they sound good and then all you would have to worry about the amp.kenwood, fosgate, pioneer, alpine all make shallow subs i have 2 kenwoods. and usely the sub you buy comes with specifications for the size encloser you need. hope this helps.
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How much sub do you need?

Some of the high end companies like MB Quart make a 6" sub you can install in your back doors if you mount the speaker on the OEM grille...