I'd probably put the swarm on top, but have no real argument as to why that would be better than putting it on the bottom, or if it even matters.
I think the only argument for allowing them each their own entrance and not keeping either totally blocked in would be the potential of over heating. Not sure what kind of temps you're having, but here is south Louisiana you run the chance of cooking your bees before they complete the combine if you don't give them each their own entrance. For this reason alone, I always give each hive an entrance when doing a combine.
No need to use a branch to help them reorient, a 20 mile move will clue the bees into that automatically. The branch trick is for shorter moves, under 2 or 3 miles.