Psychic, Danner, and Sean all make excellent points, and I'll add only a few minor comments. First, however, I'll second the "do it by ear" method of adjusting the subwoofer output. I have two Vandy 2WQ subs that I use in conjunction with Vandy 3A Sig main speakers.
In the 2WQ sub's manual, Vandersteen says to integrate the sub(s) with the main speakers by playing a good recording of the acoustic bass that features a "walking" bass solo going up and down the frequency scale. As the frequency of the bass notes pass through the crossover point (typically around 80 Hz), there should be no discernable change in the volume of the bass. I have used both walking bass solos and organ recordings (such as Wilson Audio's recording of the organ at St. Mark's Cathedral in Seattle) to tune the deep bass response.
With regard to subwoofer response in HT applications: there IS a significant bass boost in the THX standard, so if you want MUSICALLY accurate bass, don't use the "Avia Guide" or "Video Essentials" DVD to adjust your subwoofer.
If you have a sub that has an adjustable "Q", such as the Vandy 2WQ's, you can turn the "Q" up for home theater, and down for audio.