Due to "group delay" sound impulse leaves the sub usually 8-10 msec later than it leaves the main, even though the electrical impulse hits the sub and the main at the same time. So must be aligned by ear. Using just distance measurement doesn't work. Used to think there was something wrong with my autocalibration when it consistently made sub setting farther away than the actual measurement. Check:
http://www.theabsolutesound.com/articles/subwoofer-basics/?page=3
http://www.theabsolutesound.com/articles/subwoofer-basics/?page=3