The primer pin needs to "just" extract the primer. Caution: do not let the expander touch the case head. That's when you will feel the ram "stop" and are apt to bend things.
With the ram at the top of the stroke, screw down the die until it touches the case.
Leave the primer punch where it is or, remove it.
Screw the die down a little, smaller increments lets you get an idea for how much a complete turn is worth.
Run the ram w/cartridge to the top.
Note how much of the neck is sized.
Repeat until you are size the amount of the neck that you desire. (~1/2) for an '06 length neck. Maybe a little more for a short necked case (264 Win as an example).
I like to resize enough that the base of die at least touches the body of the case and the top of the stroke. The intent is to maintain center alignment. However, I don't think it works as the neck is already sized 'before' the die base touches brass.
Also I let my expander ball/primer extractor rod float. That is I don't tighten the the lock nut at the top of the die. Caution: too much float and primer ejector pins start getting bent.
Finally, adjust the expander ball and primer pin to "just" extract the primer.
Notes: If reloading to reasonable pressures the shoulder bump (ram all the way to the die base) every so many loads will be sufficient.
If you run 'max' pressures the case just above the base will require resizing every time. Thus a FL resize is in order every time.
Probably TMI but hope it helps. Your post suggests that you are headed in the right direction.