I recently bought a Ref 50 and just when through this process. After listening to booming from the other side of the house when the music volume was at a relaively low level. I decided to make the adjustment.
After adjusting all of the channel levels with a Radio Shack sound pressure meter(0 dB), go to the notch filter screen, "Setup Room Equalization". With the sound pressure meter move the test tone up and down the range. As you go up and down the range, you'll find frequencies that will make the needle rise pretty noticeably on the meter(mine was 68Hz).
Once I determined that this was the trouble spot, I set the "Notch" at 68Hz and took the level down to -4.0dB(where the meter registered back to 0dB again).
After this, I readjusted the relative sound level of the sub to the levels of the other channels.
The boominess that I had is gone now.
Hope this helps.