Riker,
If both of your subs are about the same distance from your seat, then you should definitely keep the phases set the same. The phase setting on your sub is not dependent on the number of subs but rather on the distance the sub is from the main speakers. The phase comes into play in the crossover slope area where the sound waves from the sub mix with the sound waves from your mains. You want the peaks from the speakers to line up with the peaks from the sub (more or less). If, instead, the troughs from the sub line up with the peaks from the speaker, you'll have a canceling out effect. The phase switch is there to compensate for this situation.
I made some images a while back to try to illustrate this.
In the above picture, notice that 360° for a sound wave is the distance of one Hertz, or one cycle of the wave.
This second picture shows the same sound wave, but it is exactly 180° out of phase with the first wave. Keep in mind that your ear absolutely cannot tell the difference between one phase or the other -- unless there's more than one wave source reaching it at the same time.
This image shows the two waves overlaid. When you have two or more sound waves interacting, the energies sum up. Your ears hear the wave that results from this "wave addition." As you know, adding a negative number (sound below the horizontal axis) to a positive number (sound above the horizontal axis) results in subtraction. The end result of this example would be complete silence.
