I leave everything on, except for once every couple of weeks. Then I'll shut down my return pump and skimmer. I'll put the food in and give the tank a good 15 - 20 minutes to 'suck up' all the goodies. Gives all the polyps a chance to feed nicely, in addition to the fish.
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.