Jim, You'll want to do a flagstone patio as a sandset or mortar set. In the case of the mortar set you'll have to pour a concrete slab and mortar the stone to it. The sandset is much simpler that you use a gravel base(depth is determined by the stability of the soil), and an inch of sand as a leveling material.
Don't put the stone right on the dirt!
If you are doing a mortar set than you may want to have a concrete contractor($) pour the pad for you and you lay the stone.
Good luck!

What about using portland cement mixed with sand and putting 2 inches of that below each flagstone?

Why is it neccesarry to actually pour a slab, all of my flag is 1 inch or thicker.

Jim

Just curious...Did you put your flagstone/portland cement on dirt and how did it hold up?