First of all, that is a nice install you got there jason. I have an identical trunk to you it looks like, I will probably end up doing something like that, as long as it can be removed easy enough in the event I have a blowout in the middle of nowhere at night in a blizzard lol.
It would be nicer to have a bigger box, make life a lot easier. I chose to get a sub that would take 1200 watts rms and sound good doing so. Only have about 1000wrms on it right now but it is enough since my front stage needs more work before I think about serious power. Plus any bigger than I have right now I would need 0/1 gauge which is a PITA on any car.
I thought of velcro too, but ended up getting a decent bungie cord for now that goes from corner to corner with that cross member. It attaches to the bottom of the magnet and really does an ok job until I figure out a better mounting method. My amp is mounted on top of the sub box instead of where I had it my last car, mounted on a MDF platform. So it hard to attach anything to the top of the box since the amp goes right to the edges.
If you are wondering what sort of ghetto talk I am refering to about bungie cords, I have the speaker in this same box:
As I was saying with my old install it was something like this: