The premium Pioneer HU does have subwoofer outputs. You can also check for a "Subwoofer Level Control" by going through the menu system on the HU to be sure.
There are options for you with enclosures. There is a "SubTub" that fits our cars without using any trunk space. Couple of Links:
http://www.newscionxb.com/135-do-yourself/8298-how-video-new-scionpro-com-sub-tub.html
http://www.newscionxb.com/131-audio-electronics/8233-subtub.html
This guy was going to make a custom setup. Not sure if he finished or not.
http://www.newscionxb.com/131-audio-electronics/8671-g-i-custom-xb-stealthbox.html
There are options for you with enclosures. There is a "SubTub" that fits our cars without using any trunk space. Couple of Links:
http://www.newscionxb.com/135-do-yourself/8298-how-video-new-scionpro-com-sub-tub.html
http://www.newscionxb.com/131-audio-electronics/8233-subtub.html
This guy was going to make a custom setup. Not sure if he finished or not.
http://www.newscionxb.com/131-audio-electronics/8671-g-i-custom-xb-stealthbox.html