I leave everything running and usually feed cyclopeeze either the day before or the same day I'm going to do a water change.
Since you have a small tank, 16g, and have a Remora skimmer where the pump sits in the tank and opposited to skimmer that are in the sump, you may want to turn off the skimmer for a little while as it may pull in a lot of food. Also if you target feed your corals leaving your skimmer on mayn't be a problem.