I've done a couple wall builds and alot of boxes. It can be done, it can look good. First you need to figure out what kind of space your willing to work with so you can figure out how much airspace your going to be able to play with. Then your gonna have to look at sub specs to decide if your gonna go ported, sealed, band, or free air. I prefer free air styles myself. I think anything but the bandpass style will work for you. Pick some subs that don't require alot of air space, run a box calculator to see what the dimensions are gonna be.
A properly speced box will make a cheap sub sound great, just like a poor box design will make a $1000 sub sound like a blown 6x9.
From what i seen in the back seat pics I would do 1 or 2 12's in the trunk about 8 inches behind the X brace, then double wood frame around the X. That will help compress the air the subs are moving and get you a better sound. Then throw the bottom back seat in, buy a replacement top seat and cut out where the openings are and sew up the edges. That will give you the custom look.
Or cut out the X brace and weld some extensions on it so you can bolt it back in place if needed. Then you could get a proper wall look going.