Derick,
My first responce is not to use it, you are putting poison in your food source and even if the super is not there, the poison stays in the honey and the wax in the brood boxes. Bees are always moving honey around the hive so the poison will end up back in the honey you and your family eat.
If you must use it, pull the super, freeze or at minimum, refrigerate it, to keeps the bugs from laying their eggs and developing. Then do your treatment, allow the super to warm up to at least 65 degrees and then put it back on.
Jim