I got shallows for supers.
When the top shallow is filled about 80%, I give another right on top. Earlier if I won?t see them for a week and flow is strong. Foundation only (from the 2nd super on, before some comb is good if excluder is used).
That way, they fill the super underneath to its extremes, which suits me fine in the extraction room.
I also give the honey a chance to be worked on and cared for by the bees! If you super underneath, moisture might become a problem. Also, if you super too much room, esp. in between.
This is of course a matter of climate, too!
On harvesting, I just KNOW that anything beneath the top super is FULL and READY (freshest nectar goes into top box, which is the only one with space). And I take it. Usually I know the end of flow and super in a way so I can harvest all supers and give new one(s). Depends on climate, system and flow, of course.