If your in no rush, then I would do what golf recommended, it would be the least work for both you and the bees.
If you want to get it done this year, I would put the empty deep between the current deep and the supers, making sure the queen is in the lower deep. Wait until the remaining brood hatches out of the supers, then place an inner cover over the two deeps, followed by an empty super and then the two supers with honey. Score any capped honey and then wait. The bees will move the honey out of the supers down into the deeps. When the super are empty you can remove them.