Assuming there is a phase control on your sub, play a test tone through the whole system at the Xover frequency and adjust for maximum volume, or alternatively wire the sub out-of-phase and repeat the procedure looking for the lowest volume (which many people may find easier to perceive)
Digital Signal Processing
Everyone integrating a sub into their system should read Barry Ober's page on subs (JL Audio Technical Support): http://soundoctor.com/whitepapers/subs.htm
The phase control on the sub just adds delay, and most of the time you actually need to delay the mains, not the subs.
There are some subs available that have internal DSP where you can delay the high pass output: Revel's new ones using the LFO software and Triad's. Or you can use a digital crossover such as a DEQX, Trinnov or pro audio unit. Or you can do all the crossover inside a computer and feed a multichannel DAC like an ExaSound.
The easiest way to integrate subs is just to play with delay until you get flattest response. It might take you some time to get there and you will never know if it is properly integrated (for example you may have just added a full cycle of delay to subs or mains and gotten a good SPL trace but the two are not in time alignment). The proper way to do it requires looking at the time domain. I look at impulse response and phase; it's not something that I have seen written down anywhere, and it requires a good understanding of acoustical measurements.
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