You will probably get lots of different answers to this question, but here's mine.......
First, if you are shooting a bolt gun, remove the firing pin, spring and whatever else you can easily remove from the bolt---Rem 700 and Win 70s are easy, don't know about others. You want to be able to feel the bolt close on the sized case without all the tension produced by the firing pin or striker spring.
Turn the size die down into the press, with the ram fully raised, until the bottom of the die is about 3/32 inch from the top surface of the shellholder. Size a case, clean lube off the case and try the case in the chamber; close the bolt, if you can.
The process is to size and try, slowly turning the die deeper into the press until the bolt closes with slight resistance.
In the beginning of this process, the bolt will close easily; as the die is screwed deeper into the press, the bolt closing will get more difficult. At the point that the bolt can be closed with very slight resistance, the die is properly positioned.
In the beginning, the shoulder isn't touched, but as the case body is sized more and more the shoulder actually moves forward very slightly. Then, you have to turn the die very slightly to position the shoulder corectly "for your rifle".
Rarely, I have had to grind a few thou from the top of the shellholder to let the die go deep enough to get the shoulder in the right place.
If you don't bump the shoulder just right, after 3 or 4 loadings, the shoulder will have moved forward enough to cause bolt closing to be difficult.
Additionally, the case/chamber size relationship is intended to allow the case to expand slightly to seal the chamber during firing. Then, the case contracts a bit to allow free extraction. If this sequence is prevented by improper sizing, stuck cases can happen, even with otherwise safe loads.
Sorry to describe building an atomic clock, just to tell the time.............
Jim