I use a bore scope (old type that doesn't use a laser or electronics ... I'm an old fart and don't trust electronic gizmos) to get it close. Then I shoot from a rest at 25 yards zeroing the crosshairs on the center of the target. Then I strap it firmly in the rest with the cross hairs centered on the target. From there I adjust the scope until the cross hairs are centered on the bullet hole. It's essential that the rifle does not move while adjusting the scope! The next shot will be perfectly centered in the bull's eye. From there I fine tune it at whatever range I want the hunting zero at.
My big bore hunting rifles are set three inches high at 100 yards. My varmint rifle is dead on at one hundred yards. My .22 rimfires are dead on at 50 yards. My traditional muzzle loaders are dead on at 75 yards. My inline muzzle loaders are dead on at 100 yards. My open sighted rifles (30/30 and 45/70's) are dead on at 100 yards. Air rifles dead on at 50 yards. All handguns with adjustable sights are set for 50 yards.