Yes BillyP is right. Ive noticed that the HSU volume knobs are sensative & going from about 40% to 50% seems to be a bigger jump in volume than the 10% it emplies. I have both of my HSU subs with their volume knobs at 10:00. I set them there before i run YPAO & leave it there because for me they fall within the -5dB & 0dB window that i shoot for.
If YPAO is setting you subs trim to -10dB then yes, turn down the subs knob & rerun it.
Now something might be happening depending on the placement of your sub. If you are getting a peaky response at your listening location, when YPAO "hears" your sub it would see those peaks & turn down the overall trim to compensate. If those peaks are are at certain frequencies (ones that arent felt) then that could be why you arent hearing the bass you want. This is just a guess of course & would have to be confirmed by measurements.
Your goal is to get your system Flat. In other words, you want all the different frequencies, 20hz-20khz (audible), to play at the same dB at your seat (if played at the same dB from the speakers/sub). Once you get your system close to Flat, the overall sound is very "full", "natural" & "pleasing". Those are probably the best ways for me to describe it. You dont feel like your missing anything, because you arent, your hearing the source the way it was recorded. Now if the recording isnt good, well thats another topic!
Do you listen to any podcasting? I do a lot & 2 of them i like are: HT-Guys & the other is AV-Rant. If you can, listen to the January 5th 2012 Episode of AV-Rant. One of the topics they discuss is AudioCalibration & the different techniques you can use. It was a very good episode. Its free so why not give it a listen ya know!!
Ive heard that an even better disc to use with the SPL Meter is one from RealTraps. The disc has frequencies 18hz-22khz & is in 1dB increments. The HSU disc only has 12 tracks that play the warble tones. Thats only 12 different frequencies. Yes they are the enough to get your system started in the right direction but there are some really good options out there. Im saving up to spend about $250-$300 on some gear/software to get my system more dialed in. Then i can dial in my friends systems as well.