Glad you're liking your computer setup!
To answer your questions, the subwoofer phase switch is used to make sure the subwoofer and speakers are "in phase" witch each other. When you get down to subwoofer territory (below say 100 hz) the sound pressure waves become quite long (only shifting positive/negative pressure 100 times a second) and because of this distance differences (and sometimes slight delays in amplifiers) between the speakers and subwoofer can actually cause the pressure waves to work against each.other (called destructive interference). Flipping that phase switch inverts the power sent to the cone, so that instead of destructive interference the sub/speakers now work together (constructive interference).
As for clipping, there's really nothing better to tell you than to watch out for your speakers sounding "harsh" or "strained." If they sound like they're struggling in anyway then turn the volume down.