To set the delay/distance for your speakers, you'll need to use a tape measure. Most receivers do distance in feet or meters, but some still use milliseconds. If yours does milliseconds, convert 1 foot to 1 millisecond.
As to the sub's phase, you want to choose the setting where the bass sounds fullest at your listening position.
With the sub's loudness, don't worry that the test tones don't sound loud when SPL meter shows it is even. All the test tones I've heard from properly calibrated subs end up sounding a bit anemic. Turning up the level of the sub so that it sounds equally loud as the other speakers to your ears will make it much too overpowering when you're watching movies or listening to music.
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