I have used a little different method than described above to adjust subwoofer phase. If you have a sub where the phase is adjustable by remote you can do it with one person, if not you will need a friend to help. First place the sub in the best position possible given room arrangement and spousal compatability. There are other threads that give good advice on how to find this location. Second, run the speakers full range and adjust the subwoofer crossover above the cutoff of your mains. Subwoofer volume should be set fairly low for this. Play music that you are familiar with while listening from the main listening position. Have the friend or use the remote to adjust the subwoofer phase thru its range while listening. When you get the mains and sub in phase with each other, the leading edge to the bass notes will be heard at the same time. When they are not, it will sound like 2 separate bass notes at slightly different times. It is very similar to wiring a mid range or tweeter out of phase. It will be obvious to your ears when you get it right. Now, adjust the crossover to the setting that you want and finally adjust level.
I don't know if this method is what would normally be done, but it worked for me. I have a Velodyne DD-12 which has the SMS-1 mentioned above integral to the sub. I tried going thru the set up that the manual described, which is similar to what others have suggested above, and just couldn't get it to sound right. It now blends beautifully with my mains. The fact that it also has a digital parametric eq to help smooth out the bass due to less than optimal positioning is icing on the cake.