Welcome Sitting Bull:
I would dig down 12" and make sure the hole is drained to one side or corner. Then add 9" of limestone which will allow watre to drain down away from your patio to be drained away. Then 3" of sand will give you a good base to put the flagstone on.
Do you plan to cement the joints or leave the flagstone floating? I would prefer the floating because each stone can then be corrected, should it get out or level later. Finally, spread sand over the area and sweep it off the stones into the cracks and buy some Round-Up or salt for the vegetation that will come up in the cracks.