JL makes great subs, in particular the room correction is outstanding.
Anytime you work with bass traps or any absorber you are changing the tonal balance somewhat. Excess bass trapping makes speakers sound lean, while an excess of reflections make the system sound bright. Tuning a room is a balancing act.
Also, check out the AM Acoustics room mode simulator. Try to keep your speakers and listening location away from the lowest room modes if possible. That is a great first pass at tuning your room.