Depends really what sub you have.

I have a 12" tube in the boot, pushed right up against the lights, I have my makeshift toolbox (a cardboard box) inbetween that and the seat. My amp and multichanger are simply just velcro'd down, and my halfords toolkit is up against the amp.

If you just have the sub and amp, and nothing else, then i would bolt the amp to the sub (if possible) and then maybe find some way of securing it. In my 3i, I screwed both my amp's at the time to the back of the seats, and I had a 10" box and a 10" tube strapped together.

Other thing to look at is the wiring