I'm guessing the rear seats had to be unbolted to get that box under there? You should also look into making a box that's only under one of the seats so that the other seat can still be folded down. I would really hate to lose that functionality.
I'm guessing that since the rear seat of the two door resides in between the wheel wells, the available space is too limited for a pair of subs, but it may still be feasible to make a single sub enclosure with some space for an amp to be mounted onto it.
'09 X Unlimited, 4WD, auto, half-doors, soft-top
RC 2.5" Series II BB, JKS Quick Discos, JKS adjustable front track bar
15x8 Unique 297 (Soft 8), Goodyear MTR/Kevlar 35x12.50R15
5.13 gears, ARB front locker, Currie front shafts
Bushwacker flat flares, Rubicon rails with steps added