Hi Dan, Yes, the mat should go on top of the brood box. This will help to contain the warmth through winter. There should be a 1-2cm gap around the edges of the mat to allow the bees to go up into the super for get the honey stores when they need it. The hole in the inner cover should be blocked, you don’t want your bees going up there unless you are providing food for them. And if your super is empty then remove it and pack it away for next spring. The unused space in an empty super will suck the warmth from the hive which will mean the bees have to work harder to keep their space warm and in doing so will consume more honey stores.