How long has your tank been established? You don't want to remove the fine grains of sand and thats exactly what your PF will do to you. The bacteria is what binds the finer grains of sand together and keeps them in place.
i agree with the let the filter just move the water and not let it trap any goodies. either fine grains or bacterial wastes. it will take several days for it to settle. it makes you wonder if it ever will.
The fine sand granules have so much more surface area per equal volume (more granules with more surface) that act as the substrate for bacterial biofilms to populate. This will start out as a series of nuisance blooms, but will change over to nice clean sand one the competition for new real estate is established and your tank matures. Think of the coming algal blooms as growing grass for the "next level" of consumers in the tank. Primary production must occur first before more complex life forms can be supported. Keeping the fines makes it occur with greated population densities as each specie blooms. You are encouraging complex food chains from the bottom up.
I actually run the filter with a very coarse filter plate (mine has those plastic screens to sqaush the filter material in between) it wont catch the fine particles but seems to help calm everything down.
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