Sure Dumar,
The subwoofer augments or takes over for the low frequencies where the mains drop off, but there's usually still a little overlap between the two in the upper bass frequencies.
Although both your main speakers and the subwoofer are all getting the electrical signal at the same time, they don't physically respond at quite the same rate due to mechanical and electrical differences, and a delay in one can put them out of sinc.
When your subwoofer is out of sinc with your main speakers, it can actually cancel out the upper bass instead of adding to it - that's called phase cancellation. Without that knob, your choices for tweaking are to reverse polarity on the sub and see which way sounds closer to being right, then to move the whole sub around until you find just the right spot.
By moving the sub, you don't correct the phase mis-match with the mains, but by giving the sound wave a different starting point you can bring the arrival of the sound waves in harmony by giving one a head start. The phase adjust knob on your sub saves you all this trouble, and allows you to electrically vary delay the sub output so you can tune it just right.
From the chair you'll be listening from, you need to sit and direct someone else to turn the knob to different points while listening to either an audio setup CD or a good music CD. If you don't have an assistant, you'll be getting up, moving the knob a bit, sitting down, then getting up again because you can't judge the phase from the sub itself, you'll want to align the phase so it's right at the listening position.
Hope that helped. Happy tweaking!