The litter box goes in one end of the bottom of the cage, the water and food go at the other end of the bottom of the cage. The second level should have sleeping and play areas with things such as a bag or some sort of soft, partially enclosed area. I put in some baby blankets since ferrets often bundle themselves up. The cage should be some sort of wire cage with a wire bottom and a tray. The better ones have epoxy-coated wires which makes the wires feel softer.
Ferret feet get sore from too much exposure to wire-bottomed cages.
The carpeting really helps make the sleeping quarters more pleasing to them. Why not carpeting on the lower level then you may ask. Well, when ferrets eat, food often falls around the food bowl. Water also drips and spills. If you have carpeting, food and water will just sit on the carpeting and rot instead of falling below the wire bottom of the cage to the tray.