Sorry I've never seen this part of the Rational site before, didn't even know it existed
Aligning subs by phase response can be difficult if you can't get "clean" measurements.
I'd advise practising phase alignment at higher freqs first, grab a two way box and a processor you can mangle syart around 1kHz with something easy Like LR24 slopes.
Just looking at the outputs of the crossover can be interesting to start with then add a speaker to the mix and practice.
Once you start heading south of @250Hz the wavelengths start getting much longer and sound is no longer behaving "ray-like" but more truly "wave-like"
Learning what the Phase response is telling you is the most important thing. "When did which energy arrive when?" Where the Phase slope is horizontal is where Smaart's delay time is aligned to, you can manipulate this. I like to think of it as the "phase focus control" then I can see the relative time differences between different freq's.
It's a lot easier to show than explain, get to one of Jamie's or Harry's classes once you see it it all falls into place.
I've been cruising this site and laying waste to my brain cells as I soak up the knowledge that is on this forum. I'm just a padawan to your Jedi but working on my skills with the force everyday.