I use the Magneto Speed to get my MV when developing a new load. That gives me a number to put into a ballistics calculator, that gets me close. After that, I shoot on paper at 900 yards (it's what I have available) and adjust elevation until POI is correct. I then go back and change the MV number in my ballistics calculator until it gives me the elevation that matches my scope setting.
I know Frank mentioned changing BC, but I've just never done it that way. Lots of people do.