One or two trays (the most "downstream" trays) will generally have some sort of media as a "home" for the beneficial bacteria... rough ceramic rings, balls, pellets are commercially available... but anything that will stay in place and provide lots of surface area will work. (These never get replaced, and allow a place for the bacteria to live, so you can replace the fiber filter pads every couple months without worrying about spiking the ammonia.)
One tray with activated carbon if you like that. (the most "upstream" tray)
Remaining trays stuffed with a polyester "floss" of some sort... expensive (designed for that purpose) stuff from the LFS, or cheap stuff from the fabric store... you can pack it in fairly tightly (as long as water can still be pushed through it) to provide whatever level of fine-filtering you desire.
There really is no "one right way" to use a canister... a lot depends on personal preferences and the tank and the water you're working with.