yrots: I would shake them into their permanent location. You can place a queen excluder between the brood box and bottom board to 'trap' the queen, and hopefully deter the rest of the rest of the bees from leaving her, but even that is no guarantee the bees will stay. Then leave them alone. Feed from the inner cover as you suggest. Are you using SBB? If so, I suggest sliding the corrugated piece in until they settle in. I am sure others may have other ideas. Good luck!