We generally recommend having a brood chamber of 2 deep boxes, or 3 medium boxes. If you were to use a queen excluder in your hive, you would place it on top of the 2 deeps or 3 mediums, and then super empty boxes over the top as the hive expands for them to store honey in. Any additional boxes of honey on top of those 2 deeps or 3 mediums will be safe for you to harvest, and if you use a queen excluder, you will be sure the queen has not been laying any brood in those honey boxes.
I hope this helps!
Rebekah + Bee Thinking