Help ... Totally stuck (subwoofer topic)

Hi, folks. Hoping you can help me here. Earlier this year I got a JL Audio e110 sub for my two channel system. Using a pre/power combo - no receiver. Set up is B&W N804 speakers, BAT VK-3i preamp, and MF A300cr power amp (225 wpc). Old equipment, I know, but it sounds really good. There are two issues which I can't quite figure out. 

First, I use the second output on my preamp into the line level input on the sub. I DON'T use the sub's line out into the power amp because the sound becomes very thin and unengaging. Essentially, I am running the mains full range with the sub doubling the bass. JL Audio specifically recommends that the sub's line out be connected to the power amp's inputs for a better sound. However, that's not occurring in my system. Any thoughts on why this is happening?

Second, in the configuration I use, I find that turning off the internal crossover actually brings a fuller, louder sound with more detail. Am I unknowingly biamping with the sub used this way? Seems like a waste not to use the crossover, so I have no clue as to what's going on.

I am really stumped by this, and could use your collective help. Thanks.
The problem could be phasing, i.e., when you hook the sub up via the line ins/outs, the sub is out of phase with your main's woofers. Have you tried adjusting the sub's phase control, given that it has one?
Yep, both the xover and the phase needed to be re-set once I switched to using the sub's line out. I set the xover to 80Hz and phase to 40 degrees. Now, it sounds really awesome. Much greater headroom for the highs and mids, and the e110 really digs down deep without any bloat. Those things, coupled with my having put in a set of new tweeters, is really making me love this new sound.