JL Audio Fathom

I wanted to come back to this after some thoughts.  One of the very important reasons JL subs sound so good is the quality of the built-in room correction.  I really like the choices it makes, but at the same time you can do the same with a microphone, Room EQ Wizard and miniDSP for a lot less.

If the OP is genuinely interested in going to the next level with his setup, I'd encourage him to go that route, which is going to be a lot less expensive but also more challenging.  The good news is he can't really break anything that way.

As I mentioned before though, bass traps when needed can really help, but that would come from measurements.

Leave it alone. 

Two reasons, too many complaints about JL Audio reliability, as well as how hard it is to integrate a sub with main speakers.  If you have it dialed in don't touch it!! :D

If you want to really dive in though, consider a miniDSP along with the appropriate measurement gear to help you get to glory.

Also, room acoustics matter.  A reflective room, bad placement and big room modes should be dealt with.