If you have mediums for honey supers put them in those and start there. If you want to run deeps put the deep on top of the medium, get comb drawn in that then reverse the boxes later in the year.
When you place the deep on the medium let the bees draw it out. When the queen moves up to the deep put a queen excluder on top of the medium. Once all the brood emerges from the medium you can do what you want with it.
So they'll just move up into it?
Why put the deep on top? Just put the deep on the bottom and let the bees do what is natural. They will move the broodnest down when they start filling the medium with honey.
Would I not end up with brood in the honey super?