Alright man, I won't leave you hanging here.
Yeah, you could modify the "trapdoor" (cargo floor door). Personally, since the whole cargo floor is removable, I would just custom build the entire amp housing.
A lot of guys rip out the entire cargo floor and create custom storage for wheelin' gear, air compressors, etc. No reason you can't do the same thing. It just takes the usual assortment of hand tools/ screwdrivers, etc. Completely reversible.
Look around here and on the other jeep forums for ideas.
If I were doing it, assuming you had a router, use 3/4" MDF with 1/4" recess for 1/4" plexi. Use a good black silicone to mount it in, maybe some socket head cap screws for jeep worthy bling.
EDIT: Check this link for an example: How To: Build a False Cargo Floor in WK.