I think the best way to zero one's sights is to get a shooting zero first at 100 yards. Then lower your sight's elevation whatever's needed to move impact down equal to bullet drop at 100 plus sight height above bore. 3.5 inches is about right for most scoped .30-06 rifles. This puts the scope's reticule axis well aligned with the bore axis as far as shooting is concerned. Finally, loosen the elevation and windage adjustment turrets, move them to zero then tighten them. Now if you need to come up 25 MOA to zero at 600 yards, just move elevation up that much from zero.
If one uses a 20 MOA rail under their scope, they should still be able to zero at 100 yards. And coming up 45 or so MOA to zero at 1000 will still be within the scope's reasonable windage adjustment range. But you'll have to check your scope out to see how much windage you have on both sides of zero; there's usually more on one side than the other.