Good question, I'm going to do each corner from underneath, a royal pain in the butt, but it is possible, then on the top, I'm going to take my gallon of duraglass, and fill in the cracks, once the sides are sealed, I'm going to take a 2x4 and put it along the back of the trunk, I will seal that with glass/duraglass then put the final panel in place, it can be sealed with glue.
I will then add 1-2 more layers of mdf on top of the and maybe a layer or two of glass, cut out the hole for the speaker and continue on with the box.