Perfectimage is correct. Essentially, the respective cones of your main speakers' woofers are moving either in or out in response to the music signal (provided they are connected correctly, in phase with each other). Now the cone of the subwoofer can either move in the same direction at the same time, which would result in bass reinforcement, or it can move out of sync with the main speakers, which usually results in partial cancellation/attenuation of the apparent bass level. By reversing the phase, you are attempting to put the respective motion of the sub and main speakers more in synch with each other. In reality, because of the different physical positions of the respective bass drivers, the sub could be ANYWHERE between 0 and 180 degrees out of sync with the main speakers. That's why subs having a continuously variable phase pot makes the most sense.
If you are free to move the sub around the room to find the areas of maximum bass reinforcement, that is another way to address the problem, but most folks like to put the sub in a spot where it is unobtrusive in the room. One could reverse the positive and negative speaker leads on the main speakers to put them 180 degrees different, relative to the sub, but having the main speakers out of absolute polarity might make them sound unnatural on some material. If you are using the RCA line input on the sub, then there is no way to electrically compensate for polarity, unless it has a phase pot or phase reversal switch.
I find that with multi-channel systems all these phase/polarity synchronization problems between the respective front, rear, center, and subwoofer channels are compounded. If you'd like to do an interesting experiment, just put the center channel out of phase with the mains, or connect the surrounds in opposite polarity to the fronts and see how the sound quality changes. :)