mine is set up like yours sorta, i have a box a bit bigger than yours , slot ported with a 12" infinity dual voice coil and a jbl bp600 mono amp.
i went on the speaker builder forum and told them how tall and deep my box could be and they told me the sizes of all the peices and i cutt em, glued and and nailed the box up with my air nailer. the box looks getto but its bad azz, i used old counter top mdf stuff

 

heres a pic of mine i geuss its not as long as stang8689's but i think its alot deeper cus i have like 1 inch clearance before its to deep and hits the top of the hatch. keep in mind if u do build your own demensions are important for proper resonance, go to a speaker builder forum, the have forumlas that do the math for u
ive built boxs before and they never sounded good till i used the formula for proper resonance

 

stang8689 has the right idea, in my first hatch i had a single 12 with a ported box (sounds better in a hatch then a sealed box), pretty easy setup, just build or buy a box and throw it up against the back seats with the sub facing the tail lights (sound reflection), and if you go big you'll need new window seal, you could watch my glass move back and forth a half inch with the subs hitting (untill it cracked) and with new glass i got a new seal and no problems

 

here is my setup. Its not a good picture though. I custom made the box. its heavy as crap too. 3 JL 10w6's v1 with a brutus 1600 amp. They hit pretty freakin hard. I'm trying to sell these too...

 

yeah that looks nice, i need a second sub, mine cant handle my amp for long periods before i smell it. 600rms watts is alot to push into a 350w infinity reference series, its dual voice coil in parralel so maybe its 700rms i dunno, but my amp is 2 ohm stable and the bp600 is a brutal amp, it puts out about 600rms at 4ohms according to jbl, so im tryn to think of ways to really let it do its thing. 2 subs are probably a better way to take all the power. i have it turned way down right now. sucks cus i want to crank it

 

i don't think the glass will break, maybe if i had w7's. Its also nice cause nothing moves when i am flying around corners

 

yeah mine too, plus its so heavy it doesnt wanna move. it dint even move during my accident

 

check these out, if you don't want your rear seat...
http://mustang-rear-seat-delete.com/index.php
they aren't cheap, but look like a good fit.

 

iv got 2 12's in my trunk facing the back seats. the amp is on the floor next to the box it thumps harder than crap!! they are JL audio.