I recently built a custom box for a single 10". I used 3/4" MDF from home depot, and it worked out really well. I used polyurethane glue which expands as it dries so there are absolutely no cracks. For the hookup block, I followed car toy's suggestion to just pass the wiring through the side of the wall of the box, and use a little silicone to seal it up. I bought some 2x6 foot carpet and used glue and staple gun. It turned out great. My only complaint was the stiff wire I used is somewhat of a paint to route.

I even have a spare 2x4 foot sheet of MDF you can have. I bought two, but only used one to create a box for a single 10". I believe for the best sound, you will want each subwoofer sectioned off. So you can build in a divider into a giant box. The hardest part is the flat area for the amplifier. It should fit just fine, but just depends on how visible you want it to be, and how much room you need.

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Proud owner of a Black 2003 Ford Ranger EDGE . Regular cab, 3.0l, 5spd manual, 2wd, 4.10's. Added Security, tint, step bars, Gibson SS Cat-Back exhaust, adjusted bumper, fog light mod, Jensen 75x4 watt amplifier, (4) Polk Audio EX368 Speakers, 200W MTX Amp driving a Sony XS-L101P5 10" sub in a custom box.
Future:
Line-X Spray-in Bedliner, ARE LSII Tonneau, JBA Ceramic Headers, and possibly a 3" Body Lift.
-= PICS OF MY TRUCK =-