Ok, so the reason I built the boxes the way I did was A: because they fit under the seats and the subs fit in, and B: because they were easy to build and could be taken in and out easily if I need the space.
Some of you may be concerned about the seats hitting the boxes... They do touch, but hardly at all when the seats are pushed back most of the way. One of my friends who is 6'4" got in the driver seat and adjusted the seat to his comfort level and the seat just touched the boxes, so no worries there. If someone taller sits up front and needs more space it is easy to slide the boxes back.
Concerns about the boxes and being kicked/damaged from shoes...etc.
1) The boxes could prob hold my Pat. they are so sturdy. I midered the side edges and the top of the box using a special box building mider/router bit, and the bottom is rabbited in all glued and nail-gunned in. I used a bananna-clip plug port which is siliconed and screwd in, so the box does not leak at all. I also put in some poly-fill to help with the smaller box size.
2) Instead of carpet, which would hold moisture against the boxes if water from rain or people's shoes got on them causing them to swell, I used several under coats of flat tan spray paint and then a few textured paint coats. This will keep the boxes safe from water and they don't mess up very eaisly.
Concerns with the heat build up from the amp... The way it is mounted in the spare area allows air flow to go on both sides of the amp, actually keeping it just as cool as if it were in open air in the trunk. I put a strip of velcro across the back edge, just next to the back seat, so the amp wont slide or fall but can be easily moved if I need to take out the spare.
Hope this answers most questions!