The oversimplified answer is that it controls whether a positive voltage should cause the speaker cone to push forward or pull back. Assuming it's right next to your regular speaker, you want the subwoofer to push forward the same time as the regular speaker. That would cause both speakers to work in harmony. The other phase would mean the subwoofer is pulling back while the regular speaker is pushing forward, and they would try to cancel each other out.
Of course, it gets a lot more complicated when you move the subwoofer away from your stereo speakers, as most people do. In which case, yeah, just play with the switch until it sounds okay from your chair.