I always just add a new super on top of the others when a box gets 3/4 of the way full. I have hives several supers deep right now and some with only two supers deep. Just add them on top.
It may or may not work fine. Honey acts like a queen excluder so if you put an empty under your full super the queen could move up into that and start laying. If you stack them on top of the mostly filled super there is much less chance of this happening.
Depends on the conditions and the hive. If they're just happily filling supers and you're not behind in your supering, then top super. If it's still early in the flow, and you didn't have enough supers on and everything is full, then you place it under, and maybe another on top.
You have to stay one super ahead. Nectar is 85% water. Honey is only 15% or so. So it takes almost two supers of nectar storage space to make one super of finished honey. Don't short them early in the season when there's a strong flow coming on.
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