First and foremost, before you start tweeking the phase, make sure your mains and sub are level matched. I am assuming you have taken this step.
That phase knob setting can make the difference between high SPL base with good frequency repsponse or completely the opposite. Placement and distance difference between then mains and sub are what generate the need for this control. The aim is that when the acoustical wave from your mains reaches your ear, so does the acoustical wave from the sub. When set correctly, you will not be able to tell that the sub is outputting any sound since the ear has difficulty in directionalizing lower frequencies.
If the sub is located on the imagenary line joining the mains and between the two, its easy, the knob stays at "0". If not, then here is what you do.
Take any CD with good bass like in Jazz or Techno (if you are into Rock, from personal preference I recommend using "A Perfect Circle - Thirteenth Step") . Start with the phase knob on the "0" setting and start listening. keep moving the knob in small increments and re-listen to the selected passage. The setting at with you cannot tell that the sub is playing, the bass appears to come from the mains, is where you want to leave it. If you are not being able to decide, change what you are listening to.
The difference between the correct setting and incorrect setting is fairly apparent.