Here are the plots. The first plot is of each sub by itself taken from the center LP and R+L subs from center position.
Time aligned but uneqed response across the 3 LP
For the EQ, I chose the slope of the bass to be +10db higher between 20 and 30 Hz and be down at 10 db at a 100 Hz based on the Youtube video stating that the lower frequencies (20-30) need to be 10 db louder than at 80 Hz, aka house curve.
I've listened to music and some BluRays and I must say that I agree with the slope philosophy, The bass is no longer boomy but the floors are rattling because of the lower bass. I'm actually quite pleased with the results.
Now integrating this with YPAO was a process I had to think about and run a few measurements. What I ended up doing was disabling the two sub outs on the miniDSP and running YPAO. I also ran YPAO for the main or center LP as I did NOT like what its was doing when I ran it across the 3 LPs. I realise that this would set the mains to large so just for shits & giggles (my favourite English expression) I ran a measurement as shown below.
I enabled the sub outputs on the MiniDSP, went into the AVR config menu, set the bass to sub only, set mains to small, and set the cross over to 90 Hz..(I experimented with that and 90 gave me the best result) . I also played with the sub distance and found that 10.5' gave me the best response. I also took a measurement of YPAO set to through which means no YPAO EQ but bass management is still employed.