HTL- That's what a parametric eq is for.

(Smoothes the room-induced peaks in a sub's reponse. Behringer, Rane, Symetrix all make 'em. I have a Behringer DSP1124p. Really cheap, and really flexible.)

Phase is easy. I've found using a discrete test tone disc is the easiest way. www.stryke.com

Set up all the BM the way it should be. Then play tones at or near the crossover freq. Adjust your sub's phase adjustment (when a switch, or a knob) until the output is the loudest at your listening position.

I've tried the Avia test signals for phase, and I still believe that discrete test tones are easier to use (with a sound level meter of course).