I don't know if you're still looking for an answer to this, but for anyone else who comes along, in the output options dialog, change the priority order so "Pass" is first. The programming will machine each tool pass in order. For example, if you have a .25 end mill with two passes (main cut & final pass) and a .125 end mill with one pass for detail, you will have the tools cut in the order of .1) 25 end mill main cut, 2) .125 end mill, and finally 3) .25 end mill final pass.
Hope that helps.