Rhythmic F12SE setup using line in

I would prefer to dial in my sub without the use of the minidsp. 

I totally sympathize and tried for a very long time -- arduous, even onerous work -- to measure, move, listen, dial in and out, etc. to get the bass right. A good friend of mine who's been an audiophile for 30 years with an incredible and well-designed system (he also builds audio) has DSP for bass. It really does not "pollute" the sound in the way that many worry about for the higher registers. Keep in mind, this is limited to the subs only.

In other words, the benefit gained by dialing in subs (and room) far outweighs the (actually small) detriments of adding dsp to the system. For me, this was evident enough to help me reconsider and reject my bias against dsp.

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?

Placement of speakers and sub, not to mention chair placement, can have everything to do with clarifying  the low end, and everything else.  Maybe you have limited options to do this?

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.