Matt,
I use the threadmill manufacturers spec for the diameter which is the small end diameter. it is a straight tool even though it is a taper pipe thread in my setup that seems to work. Notice that I have a large number of flutes. I think that detemines the thread depth that it will cut (not sure I don't remember). I set this up quite a while ago and made a template and haven't changed it since.Just bring it into the MFG file and select holes and run.
As far as thread diameter there is a parameter for that.
hope this helps
Steve