Congrats on the Sexplorer. I have an 04, and had a 95 before that, and I have really enjoyed them both.
I run a box with 3 10s, and at one time had 2 12s. These were sealed boxes and I pushed the box against the seats and fired towards the hatch. Firing them up, forward, or moving the box further back made it quieter inside. I can't speak for the results with a ported box, but I plan on doing two ported 15s soon enough, so I'm also interested in the best way. I assume subs and port both pointing to the rear would be best.
When I wrecked my 95, it was a high speed collision with the box in back not bolted down, and it didn't come through the rear seats. I guess if you hit something hard enough or start rolling, the box could really do some damage. Personally I just don't worry about it.