I cut the entire inside panel out, from the rear corners up to where the rear seats fold back to. I made the top and mounting face with 3/4" MDF to give me the approximate size I wanted, and fit pieces of MDF inside the cut fenderwells to make the sides. The back wall of the enclosure(s) is actually the outside skin of the fenderwell, with something like 6-8 layers of fiberglass mat stiffening it, and sealing it to the MDF of the box. All told, I've got about 2.4 cu ft per enclosure, which equates to about 2.0 cu ft after port and driver displacement, perfect for my old-school Celestion AD15-H's.... that's right, 15" subs in 2.0 cubes, can't do that with ANY of today's long-excursion subs.
I recessed the subs into the enclosures, so that I could make covers out of some 3/8" plywood to protect them. Drilled a bunch of 3/4" holes in a grid pattern to allow for air movement, and covered the cover with some acoustical carpet.
I've also got a pair of Powerbass S-10 subs in my center console I fabbed up, firing downward. I made brackets to move the seats out and back 1 1/2", I now have about 14" between the seatbelt mounts. Made an amp rack to fit on the floor from the dash to the back of the front seats, I have 3 amps mounted on it. The Powerbass subs are in a 2.0 cu ft enclosure (I think??), and fire downward at the amps, with about 1/2" of clearance between the cones at max travel and the amps. I had enough room to do a flip-open lid in the top of the enclosure, I can store about 20 CD's, and all my paperwork for work (as a contractor). This enclosure is squared-off, but the front face slopes down towards the dash, leaving me access to the power ports.
Been in my truck for about 4 years now, still going strong.
My next truck will be a Suburban, I plan on doing another center console the same way, but will do it with fiberglass and body filler, I want it to have a more rounded look to it.
that sounds like one hell of a set up... love to see some pics