Within a swarming mass of bees, it is difficult to actually locate the queen, it is a lucky day when that happens. The beekeeper must be patient and watch. The cover of the hive is placed to create a minimal exit/entrance to the hive. Drawn combs of honey or, better yet, comb with brood in it, are ideal motives for Queen and bees to stay. If the Queen is inside, the bees will follow her into the hive.
This is exactly what happened... all of the bees began to march through the entrance to the hive. She was clearly inside....
Photo courtesy of Ben Fisher