The beds in the hybridizing area and seedling beds are 10" deep, we use 2x10s. The others are made of rocks and they are anywhere from 12" to 3ft deep. If you notice when you dig up a daylily that the roots spread outward more so than downward so 10-12" deep is plenty good.
Pine Bark (the small dime size or nickel size pieces, not the shredded or big nugget size) mixed with about 10% sand is what most nurseries around here use to pot up cuttings or seedlings or plugs and such. Then you can add whatever amendments you want such as chicken litter, alfalfa pellets, fertilizer, and whatever else you may want to use.