Xerox - I feed the bees the exact way you describe. I've never had bees "move" into the empty upper box, even thought they can get up there. Iddee's right, it "can" happen. I'd keep an eye on them, but I like having a small open space next to the jar, for the odd bee that gets stuck up there when I'm refilling. If they started to move en-mass up there, then I'd close it off, and/or give them more room below.