My understanding is that it will filter SOME of the polyquat out, but not all. If you add it to the skimmer, you will lose more than if you add it to the return stream. The more it distributes throughout the water, the less you lose.

Quite frankly, when I close, I don't bother worrying about it filtering out--the FC drops sharply (normal) which tells me the Polyquat is well-distributed. I then raise FC to where I want it. It will HELP to bypass the filter, but I don't believe it's necessary, especially if you add the Polyquat to the return stream. I say this because it hasn't been a problem for ME when I close my pool.