Without access to an analyzer I recommend using a warble (Bink test CD) instead of a sinus when attempting to align by ear.
This way you at least hear all frequencies of interest throughout the XO region.
Like Ivan pointed out, using a sinus you might very well end up being in phase for that specific frequency and still be anything from 1/2 cycle (polarity reversed) to numerous cycles off.
The result will be ripple to the left and right of the XO point. The frequency range where this ripple occurs is determined by relative level and the severity by the amount of misalignment or difference in phase slopes.