Last time I inspected our best hive, I smoked from the bottom and removed the migratory cover. 15 minutes later the inspection is done, I had not seen the queen, and I picked up the migratory cover to replace it. And there is the queen, along with maybe five workers... just sitting on the inside of the cover. I VERY CAREFULLY replaced the cover, trying not to crush the queen.
Since then, I've been smoking from the top. :-D