Re: what should be where ?
They usually have brood in both boxes, the queen would move up in honey super also if you have no excluder.
Honey is usually stored a bit more in the upper box. I'm guessing two boxes is your,...so called brood box, this is also our set up here.
One's these two boxes are full, then surplus honey, [above] can be harvested, never take honey away from the brood box.
See this set up,..just harvested the first crop.
Grow shrubs & trees,...it's good for bees!