measuring bullet round out

I am new to measuring bullet and case runout.
Where does one measure the bullet runout and case runout?
What tolerances do you use for Benchrest, highpower?
I have the Sinclair tool to measure but only have an indicator that will go to .001.
Primarily measuring 6 Dasher, 223, and 308.
Thanks

Assuming this is a v-block type gauge:
You can measure on case necks for case runout.
You can measure just in front of case mouths on exposed bullet bearing for loaded runout.

A real runout limit is dependent on chamber body & neck clearances. If you're neck clearance is say 2thou, then 5thou of runout is not good.
You'd be causing a chambered pressure point that could throw shots.
And before you think like many do, that higher clearances will solve this, keep in mind that it is high clearances/hi sizing that causes runout.
Very little clearance with minimal sizing leads to incredibly low runout.
But either way, it is actually difficult to make bananas bad enough to throw shots. You have to go out of your way to screw it up that bad.

That indicator accuracy is fine enough to see good from bad here.