Scope height after zero

I am seeing to measure scope height after zero as well as velocity at a couple different distances. If I get sighted in at 35 yards then I need to get scope height? Or is it measure my scope height before and input it into the ballistic app? I’m just not understanding getting a scope height after I zero?

Also, if I run a magneto speed and only able to get a velocity at the muzzle how would you get the velocity at say 50 and 75 yards to input that information in the app?

Thanks.
 
I am seeing to measure scope height after zero as well as velocity at a couple different distances. If I get sighted in at 35 yards then I need to get scope height? Or is it measure my scope height before and input it into the ballistic app? I’m just not understanding getting a scope height after I zero?

Also, if I run a magneto speed and only able to get a velocity at the muzzle how would you get the velocity at say 50 and 75 yards to input that information in the app?

Thanks.
Measure your center of scope to center of barrel and enter this in the scope height in your program
Note after zero then take a shot at 10 yards to verify it matches your apps holdover point - if not adjust your height in the app to make them match
 
Diagram shows correct method, especially important if you are using adjusted mounts, diagram is exaggerated for clarity:

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