As for your new packages, I would start them in a single deep. When 8 of the 10 frames are drawn, add a second deep. When 8 of the 10 frames of the second deep is drawn, add a honey super over a queen excluder.
As for your existing hives with brood in your supers, how much brood is up there? If there is only a frame or two, I would insure the queen is in the lower boxes and place an excluder between the brood boxes and honey supers. When the brood hatches they will fill with honey. As the queen needs more space, she will move down to the lower box.
Good Luck,
Steve