Stringreen, sub level is certainly important for proper integration, but turning down the level on a misaligned sub won't solve the problem, it will just make it less noticeable (along with the bass).
Shadorne, I disagree "that you can't perceive accurately what is happening to the bass response except by what it 'masks' in the higher frequencies." If you consider a single frequency around the crossover frequency (say, 80 Hz), it is being played by both the mains and the sub(s). Those outputs will either sum properly, or not, and you can easily hear very small changes in delay. (As an experiment, try playing a constant tone and turning the phase knob on a properly-aligned sub while watching an SPL meter.)
But real signals are the sum of a wide range of frequencies, and the overlap between subs and mains is also across a range of frequencies. Properly aligned, the waveforms will sum together properly, but when misaligned they will smear out the low-frequency information. The effect is plainly audible, and can't be attributed solely to masking.
Shadorne, I disagree "that you can't perceive accurately what is happening to the bass response except by what it 'masks' in the higher frequencies." If you consider a single frequency around the crossover frequency (say, 80 Hz), it is being played by both the mains and the sub(s). Those outputs will either sum properly, or not, and you can easily hear very small changes in delay. (As an experiment, try playing a constant tone and turning the phase knob on a properly-aligned sub while watching an SPL meter.)
But real signals are the sum of a wide range of frequencies, and the overlap between subs and mains is also across a range of frequencies. Properly aligned, the waveforms will sum together properly, but when misaligned they will smear out the low-frequency information. The effect is plainly audible, and can't be attributed solely to masking.