Cooling multiple items on a sheet pan rack
I do not know your setup and why you'd have something above or below something else when cooling but I'll answer from a physics point of view. When you take something out of the oven and it is still hot it will heat the air around it. The hot air will rise and come into contact with whatever is above it. If that happens to be unbaked items then heat will be transferred to them, and for many things you don't want that. So if I had to put fresh baked goods above or below unbaked ones I would put them above so that the unbaked ones stay cooler. 

My recommendation would be to keep the unbaked items separate if you can as even putting the baked ones above would still heat the ones below somewhat.