If the rifle is easy to bore sight, I don't bother to reset to mechanical center. After scope is mounted, proceed directly to bore sighting. Remember to account for sight height over bore (center-to-center) when bore sighting indoors. Example: desired zero = 300 feet, muzzle-to-wall = 10 feet, sight-height = 2". Make two marks on the wall, the top mark represents the 100 yard zero, bottom mark = expected 10 foot POI for a 100 yard zero. Bottom mark is 2" * (1 - 10/300) = 1.9" below top mark. Line up bore to bottom mark, the adjust optic to top mark. It's important that rifle and marks are both plumb.
If the rifle can't be bore sighted (e.g., AR15 and I have no bore sight laser), reset to optic to mechanical center, then dial one MOA up for each inch of sight height over bore (for a 100 yard zero). Half that for 200 yard zero, double for 50 yard zero.
At the range, just to make sure I'm on paper, I'll set up paper as close as possible, let's say 50 yards. Example: desired zero = 100 yards, muzzle-to-target = 50 yards, sight-height = 3 inches. I make two marks, the top mark represents the 100 yard zero, bottom mark = expected 50 yard POI for a 100 yard zero. Bottom mark is 3" * (1 - 50/100) = 1.5" below top mark. Aim at the top mark, adjust until POI is on the bottom mark. When you move target out to 100 yards, POI should be just a few clicks lower than POA (whatever the gravity drop is at your zero range).