Usually this depends on the context.
In some tricks (e.g. Johns Bannon´s classic "Strangers Gallery") it´s a built in logic that you end with removing the gaffs from the deck.
You can leave the gaff in the cardbox and then put the deck into the cardbox after a trick, do something else and then take the deck with the added gaffs out for another card trick.
You could also select the tricks in your set in a way that the existence of the gaffs in the deck doesn´t matter for preceeding or suceedeing tricks (similar to Denis Behr´s "finding you way home"-concept for memorized deck work).
Or just switch the whole deck.
Or the obvious one: Palm the gaffs off in the offbeat after the trick (or add the gaffs respectively)
Just figure out what you want to do with gaffs first and when that´s clear you´ll probaly figure out a way to manage them.