Did this a few years back on my '03 Avy. I had a heater port and a sub in the footrest. Sawzall around the perimeter. Used styrofoam between the back part of the hump and the steering cables and other junk that was hanging out back there so I didn't cut anything.
Built a "bridge" over the hole in the floor with birch that was elevated using some plastic washers so air would flow in there and keep from collecting moisture. Coated the birch in fiberglass resin and think I plastic-dipped in black. Then mounted box with new JL sub onto the "bridge."
Later built a section next to it to hold the heater vent. Was very please with the results