There are a couple of different ways to do a spare tire sub enclosure. Usually the easiest way is to make a wood baffle that covers the entire well, and then use expanding foam to fill in the outer areas, and again on the inside edge where the baffle meets the metal. The problem is that the metal of the spare tire well will resonate so you need to deaden the metal.
2nd, You could build a partial wood, partial fiberglas enclosure, how to do that has been covered elsewhere. Its really no different in the spare tire well from anywhere else.