People have been very creative with finding spaces to put speaker boxes in cars. One of the nice things about building a subwoofer box (vs building a loudspeaker, or higher-frequency speaker box) is that the shape of the box isn't very critical - You want the overall volume to come close to the speaker manufacturers recommendations, but in the end, bass is pretty forgiving of precision [at least as far as most non-audiophiles are concerned]
For my build, I wanted to use the space in the left side of the trunk. The right side houses the spare tire, and I prefer to keep my spare just in case. Some people have made boxes that fit directly inside of full-size spare tires in the trunk well.