You have to think how bees work
They will store honey from the top down so that they can eat it from the bottom up and then start laying from the top down! The reason is that the warmest part of the hive is at the top so as they start to run out of stores then need to use less energy, if you put the stores at the bottom they will just move them to the top, a real waste of effort unless you want to empty the super.
The best thing to do is extract the super and feed sugar, as Finman will tell you honey is far more expensive than sugar!
Whatever you do the queen will end up laying in the closest part of the hive to the stores from the top.
Hope that makes sense!
E