I've had a couple different BioCubes in the past, and I always did an egg crate media rack with three/four shelves. On the top was filter floss, then a pag of cemi-pure elite, then a larger section for cheato, and then live rock rubble. Worked amazing for me. Sometimes the older BioCubes have a fully painted background, so you may have to razorblade the middle section off to get a light in the back.
This link is killer for all things Bio Cube Upgrade related.
http://www.nano-reef.com/topic/18078...esource-guide/