My understanding (and observations in my room confirm it) is that if all your speakers are set to "small" the bass is only coming through the sub. In this case there will be VERY little if any difference from changing the phase on the sub as ths sub and other speakers are not outputting same tones.
If however the speakers are set to "large" then they and the sub are outputting same bass tones and the phase will matter. Depending on the sitting position and the speakers placement the same tone may be coming to your ears out of phase from the mains and from the sub cancelling each other. If you find this is the case flip the phase switch.
In general setting the speakers to "small" seems to be consensus, probably in part because blending with the sub becomes a much easier thing across the sitting positions and even with sub-optimal speaker placement.
