Yep, that's the way I do it. there is a "finish" allowance that you can set and it will leave that much (or if you want to make the cut oversize for some reason, put in a negative amount for the finish pass) Sometimes, I will use a "rougher" mill and then switch to a "finish" mill for the finish pass.
Makes it easy to do as there are times the speeds and feeds will also be different.