The reason we added the second cup is to spread out the wear during a period when we may not be able to move the hole location. With sand based greens, the surface can quickly freeze, preventing us from "cutting a cup."
So how does this two hole system work? The idea of rotating the flagstick from one cup to the other is simple. Before leaving each green, move the pin to the opposite hole location from the one you just played. Thus the next group will be playing 18 different pin placements than you did. (Of course, if you're playing a match with more than one group, only the last group should move the pin.)
As conditions allow, we'll change the two hole locations for the remainder of the winter, and go back to just one hole in another month or so when some consistently warmer weather returns.