I thought u adjust the volume control until it read 75dbs and then continue with the rest of the calibration, I had to bypass the LFE input on my sub ( using the LFE input bypasses all controls ) and I would not have a way to adjust the volume on the sub so I use the left or right input and the volume control is set to 1.5 out of 12 to reach 75dbs and after calibration my sub trims are at -3.5. I would assume if I adjusted the sub volume control to 4-5 then my trims would be around -7 or -9 so as long as your not at -12 it really should not matter, but then again I could be wrong.
-3.5dB is perfect for the sub trims. It is high enough to ensure that auto-on works properly if your sub has it and you use it and low enough to enable you to turn the trim up a little if you prefer a 'hotter' bass. It is also very unlikely, at that level, to clip the input of your sub amp.