just some thoughts, what kinds of enclosure do u have the 12 in? what type of bass response r u looking for is the most important ? Regardless of what so called expersts tell you about either listening repsonses coming ffom your speakers it is all moot unless that type of sound is pleasing to you the owner n driver.
if u want a tight snap of a bass where it clearly hits u inthe back try a sealed enclosure, less raddle from that in the truck of a ported or band pass bass unit. if u want a rolling deep bass responses as in a ported or bandpass, try an air free sub mounted in from the tope of your read deck that uses the trucvk space as an enclosure.
Mount the speakers, box ported or not with the speakers facing directly into the back of the fold down seats. now with that being said when u do lay down your rear seats the response won't be as clear as the sound is now into and facing the seat and through that is the rear pass seats
perhaps shave down some of the stuffing in your rear seats so the sound can travel thru them more easily and the others suggestions of Dynomat-a lining sound dampening material you'd line the inside of your trunck with assist in cutting abck some of the extra reverb bouncing off of the metal of your trunk and being displaced back into your sound stage.
I'm new here, so perhaps my angle or feed back is a little dated but decide first what sounds pleasing to you bro, not what others tell you what you should like. thewn get adviuce on how to get what you want!