How we've done it is by:
1. Building a box that will go around the actual sub box. It would only be 5 sided, so the sub box can fit into it.
2. Cut the rear deck and cover. Make a grill cloth cover for the hole.
3. Make a hole about the same size as the hole in the rear deck, in the box. Not the sub box, but the secondary box.
4. Tape or fiberglass the 2 holes together. Make sure there isnt any leaks from the secondary box to the rear deck.
5. Mount the secondary box.
6. Mount the sub box to the secondary. At this point, its your choice if your going to make a cover board for the whole back, to cover everything. We also seal between the sub and the secondary box.
7. Found it works well with sealed enclosures, and if the rear window has a ample slant.
8. Tried it once with a ported box.. and all you could hear is a shitload of turbulence.
Wish I had some pics to show you, but I dont. My buddy has them all in his photo album.
Bill T.