Rhythmic F12SE setup using line in

I concur with @audiorusty.   When I had my F12s in my system, I found the sound better when I plugged the ports on my speakers, moved the speakers away from the wall, turned up the gain on the sub and turned down the cross over on the sub.  

Ok, so I better understand, I would run my sub line out from my preamp to the miniDSP, let it do its thing, and run that to the sub. My R11’s would still run full range analog directly from the preamp. The sound processing for the sub only would be based upon room characteristics & R11 output. Is that correct?

You’ve got it exactly. The diagram below could have an additional sub added and with the other miniDSP model you were indicating, perhaps more. But you have the general principle exactly right.

OK, on the bass management, I thought I would provide status. I adjusted the subwoofer, the best I could with my ears. Did not sound great, so I decided to run Audyssey MultEQ-x from my Marantz AVR running home theater pass thru my Rogue preamp, both with and without my Rhythmic. I then was able to see the problem on the frequency response graphs... something between my R11's and my room was causing 32hz peaks of +16db followed by crashes of -12db at both 50 & 90hz, something I could never adjust out.

Several of you suggested port plugs, so thought I would try that... voila... the problem for the most part went away with full plugs on the right speaker (nearest the corner) and partial plugs on the left (mid wall). I was able to then integrate my Rhythmic back in adjusting for the flattest response measured by MultEQ-x... not perfect but very good!

I may at some future date buy a miniDSP, but right now I am happy and I remain hesitant with it's ADA conversions, as I believe to do properly, i would need to set both low pass and high pass digitizing my entire range.

Thank you to everyone for your excellent recommendations! Happy New Year.