Move your sub

I've had just the opposite experience connecting my JL subs to the speaker connection (high level inputs).  It changed the tonality of my system and seemed to soften dynamics. 

Using the outs from my pre-amp has been better.  I'm now going to try actually crossing over to my mains to check that out.

 

I tried one subwoofer, but I always had the impression, real or not, that I wasn't getting true stereo.  So I added another.  Both were positioned below or next to the main speakers because I wanted the wave front to be as coherent as possible - which doesn't happen when the mains and the subs aren't in the same areas.  Anyway, I continued to use the subs when I got my Martin Logan ESLs until one day when I disconnected them and found the sound much improved.  The subs (actually sub, since on was blown by a recent power outage) are now working with a pair of Celestion SL6si's.

I’ve found Mapleshades advice to be spot on.  2 are better than 1.  Subs should be within 1-2 inches of the mains midrange drivers and either interior or exterior to the main speakers.  Subs should face along the width of the room (180 degrees) to mains.  Speakers should face the long wall with the listening position against the back of the long wall.  Speaker position should be as nearfield and separated as supports solid imaging and accurate bass response.