There really isn't much to be done (outside of DIY) for a 2 door JK. The under-seat systems are small but good for a wallet. With those i"m always confused if they will actually fit with the 2011-2012 changes some don't work with the 2012+.

IF you have a rear seat in a 2 door, the space behind the seat is barely big enough for a 6 pack cooler and a duffle bag. My solution has been to just NOT carry much if its not well hidden. Not really a good answer. One of my buddies made a tray at the top of his rear door that covers to the rear seat. Works well enough.