The sub will be mounted to the rear deck (which will be a solid piece of MDF) and the enclosure will be attached to the underside of the deck. The trunk is sealed pretty well from the interior of the vehicle. I can totally seal of the area by placing another piece of MDF across the back of the seats. The sides of the trunk aren't a problem at all.

After reading Thunder's How-To I was thinking that I can used a sonotube as the enclosure and an MDF ring at the back to hold the mat in place.