Seemed like they would fill the space since it was open between two busy areas.
they may if you have enough of a flow, long enough. how many deep do you want to be for winter? if you want to be 2 deep, then you want the majority of your brood in the bottom boxes. that will make it easier to force them down. if you want honey, you want your honey supers on the top and if they have some brood in them, that's ok. not everyone uses an excluder.
i'm thinking that if you keep your empty boxes on the top, you have an easier time when winter comes, or an easier time seeing how much they are building up...and seeing if they'll fill the top with honey.
a two queen hive is not a bad thing :-)
anyway...that's the way i'd go.