My feral hive was queenless with laying workers. I bought another hive last week and combined the two. I set the new brood chamber and honey super on top of my original brood chamber. A week later I found the queen and put her in the bottom box with an excluder between the upper brood chamber and lower, with a medium super on top and removed the top brood box, since there was nothing much happening in it with the queen below.
Anyway, now I have a deep on the bottom for brood and a nearly-full medium on top of an excluder. The medium super is now almost full of honey and does have some older brood in that will be emerging soon. I need to add another medium. Is it best to put it above the existing one, or below? The new super is foundation only, no drawn comb. I am not going to harvest any honey this year, unless they have a huge surplus. I'm going to let this hive grow in numbers and maybe split it next year.
I now have the empty deep with partially-drawn comb. What should I do with that? Store it and treat for wax-moths, or add it above the other brood chamber?
Personally, I would add the other deep brood chamber next, so they can get established in the two brood chambers.
Where I would add it would depend on the strength of the hive. They have to take care of brood, so adding an empty box between two boxes that have brood can stress a weak hive. You might want to add the empty deep to the bottom if you think they are still pretty weak.
If they are doing well, I would add the empty deep between the medium super and the deep box, because it's nice to have an empty one for the queen to move up into.