This is what I did with my sub install:
The amp board is attached to the back of the sub enclosure with a couple of large pieces of extruded aluminium joining the tie-down hooks to their original mounting points in the floor so I can still use them
I used a genuine D2 non-ski-hatch carpet so the colour matched.
Two Infinity Kappa 12s firing through the ski hatch
They use the entire boot as a 500 litre ported enclosure with the ports in the original speaker mountings in the rear shelf.