IMO, the easiest way to get subs in the GT is to simply buy a prefabbed box and sit it on the rear deck... however, most 10" subs require around 1 cubic foot in a sealed box... that 1 cubic foot is larger than it seems...
another fairly easy way, and i've been thinking about going this route myself, is to use a sub that was designed for free-air use... free air subs don't require a specific amount of air for themselves, thus no box is required... you could make yourself a baffle to cover the entire spare tire area, then simply mount the sub in the middle of it or whatnot... if you wanted to keep the tray back there, it would then only be a matter of mounting the sub either above the tray, or cutting out a portion of the tray to allow for clearance... put a piano style hinge on either the top or bottom, and you have yourself a clean looking setup while retaining access to the tray above the gas tank...