I agree with Nigel - swap the boxes over when you can. It might be a bit mesy if the bees are living between two boxes though.
I put supers under brood boxes during September (no queen excluder). The bees have time to move themselves and food around if they want to as it's not too cold at that time of year. In March or at the time of first inspection, the nadired super is usually empty of stores and very very rarely has any brood so it's easy to remove.
May your bees read the same books as you do.