I imagine you'll want your box up against your back seat facing backwards? I am planning to build a new box that will be the width of the trunk but not very deep. I was racking my brain trying to figure out a way to keep it in place, but yet easily removeable, when I came up with an idea - hopefully I'll be able to explain it well enough to make sense:
Take a long piece of metal about 45-46" long X 2-3" wide X 1/8" thick, paint it black so it will blend in with the trunk carpeting, and screw it to the back of your box. Fold down your rear seats and slide the box into the resulting trunk opening from the cabin. Since the trunk is only ~40" wide, the extra 2.5" on each end of the metal bar will lay up against the sides of the trunk seat supports. When you put the seats back up over the bar, it will be solidly held in and the sub box won't move anywhere. When you want to remove the sub for whatever reason, just put the seats down again and pull the sub out from the cabin again. This way requires no alterations to the car at all.
This is what I'm going to do, but I have a HB and I don't know how much different it is from a sedan.