I'm not getting anything from my speakers. It's all subs. Here's with the mini and taking it out of the picture. Both sweeps are with Audyssey off.
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Is that not a massive improvement?
Looks pretty sweet to me!
Hopefully it will work to your preferences to turn the sub up if you like more bass (kind of sounds like you may), but this way, your bass is more even across it's range. In this sense, your sub level is analgous to a bass control and the crossover point acts as the frequency at which the bass control becomes active.
The real question most of us want to see is what you get after Audyssey and how it compares to your Audyssey w/o MiniDSP graph!
As far as the home stretch, I think this all begs the question of where to cross your towers to the subs. You have towers with legitimate bass, so you can cross them anywhere from 40Hz on up.
Stick with the basic plan and see if the miniDSP "enabled" Audyssey to work better to see if you get further benefits similar to what ATLAudio got.
Also compare miniDSP + Audyssey vs miniDSP + pure direct to see what your ears think. Many people believe that the biggest benefit of Audyssey is all "about the bass" and would just as soon have no processing at highr frequencies (witness ADTG and L&R Bypass).
You might measure just the bass frequencies from towers - both with and without Audyssey to see how good the response is. Worst case, if the Audyssey result of the towers is wonky at lower frequencies, you may decide you would rather cross at 100Hz than let the towers compromise the output of the subs. OTOH, you are essentially running 4 subs across the front of your room so that should smooth out the response.
This can really get convoluted. If you had all 4 bass drivers in play, the corrections you applied to the 2 subs via miniDSP may not have all been needed. You could run the sweeps with all four then tweak the two subs via miniDSP to get the best 4 driver response curve.
For now, I would stick with what you have and see how well it measures. I think it will be very good!
However, you might keep a note pad stashed by your system and write down "future investigations for rainy days". You may or may not ever touch them, but it is nice to have the list there and consider if any of them look like "low hanging fruit" after you have fully acclimated to your refined tunings!