I use a pulse test with appropriate instrumentation and SW.
The simplest (quick and dirty but good enough for most) way I adjust the phase is to play a test tone at the crossover point and adjust for maximum output at the listening position. That ensures the sub and mains are in phase. At frequencies away from that point phase alignment is less critical as there is less output from the speakers as they are filtered by the crossover(s).
I would not use pink noise for this particular test because it is to "busy" to isolate the crossover frequency (where it matters).
FWIWFM - Don
p.s. Read the REW thread in the Audio Theory forum here. SW is free, you need a laptop with a soundcard and decent mic, preferably calibrated. There are inexpensive ones available (maybe $100 vs. the $1200 earthworks mic I use).
"After silence, that which best expresses the inexpressible, is music" - Aldous Huxley