Re: Best Procedure for getting all bees into bottom box
The shake method is very effective. You can sometimes smoke the top box quite heavy, then slip the qe in, but this has a lower success rate.
I have had luck using a fume board, to chase most of the bees from the box and slip the qe in, seems the queen will go down even when many nurse bees won't.
Once swarming concern is minimized, you can just wait till they backfill with honey.
Hindsight is 20/10, not 20/20...
After the fact, I always know what didn't work.