When aligning subs to mains in the impulse response, you have two goals:
1. No part of the subwoofer response should occur before the main response. If it is unavoidable, it should be low in amplitude and within the psychoacoustic threshold of inaudibility (about 20ms of pre-masking).
2. The highest peak of the subwoofer response should not occur after the main response. Ideally, it should occur together. If this is unavoidable, then it should be within the psychoacoustic threshold of inaudibility (generally about half a period of the wavelength in question).
Both goals are mutually contradictory with minimum-phase DSP. You have to choose one or the other - either the small wiggle occurs before the main impulse, or you align the small wiggle to the main impulse, then the big wiggle occurs later than ideal. One would give you "pre ringing", the other would make the subwoofer sound "slow". I prefer prioritizing the second goal because the initial deflection is small and short.
Sometimes, subwoofers have additional peaks that may be even higher in amplitude than the initial deflections (e.g. the 3rd or 4th peak). This is due to reflections and not the direct sound of the subwoofer. Some caution needs to be taken when interpreting the response.
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A good example is in his MDAT. Notice how the green subwoofer response is distorted compared to the red sub? Assuming it's the same brand of subwoofer with the same response, this is due to a reflection distorting the response of the sub. It's not so clear where the main impulse is.
Think of it this way: each speaker and sub is a "subwoofer" with different frequency responses thanks to different positions in the room. If we are talking about mono bass, then you can think of the sum of L+R mains as a single subwoofer. Every time you add another subwoofer, the sum of all the speakers and subs is a single subwoofer.
Of course you could do it the way you describe. This way is how I do it. That post will get very long if I were to go through every possible permutation of how to align subs to mains. I am a bit of a collector of different sub aligning methods, every time I see something new, I go and experiment with it. Some methods work better than others, some are easier than others.