You've got a few options to choose from:
(1) Standard sub enclosure. Just make it easily removable when trunk space is needed.
(2) Glass a sub or two in the rear corners of the trunk. But, it's difficult for DIY and $$$ to have a shop do it.
(3) You can mount some subs underneath the rear deck. You can fit up to (3) 8" subs mounted to the bottom of the deck in free-air mode. You could also come up with some other custom enclosures for mounting underneath the rear deck.
