It depends on what you are marking and what you are marking with. A pounce or chalk will rub off on a whole quilt but can be used to mark inside the hoop. If you plan a repeated motif then the top can be marked before hand with a water disappearing marker or similar. If you use the air disappearing marker, again some of your marking will be gone before you finish quilting. If you are quilting straight lines, I perfer quilting along side painter's tape.
As with any method you decide to use.....Test and remove on scraps FIRST!