I put this together quickly, but I hope that the idea comes through.
Some shooters have difficulty finding a bullet hole at 25 yd because the reticle is not aligned with the target. They put on a scope at home and head off to the range. When they aim at the bull and fire, the bullet hole is nowhere to be found. Where did it go? Worse, the amount of error increases the farther the rifle is from the target. That is why most sighting in is done at close range.
What you want to do first, even before you mount the scope on the rifle, is ensure that the lenses are close to being centred in the scope as possible. This is for hunting scopes, and will give you the maximum adjustment in all directions. It is good to do with scopes that have been moved from one rifle to another, or that you got used.
You begin by locating the mechanical centre of the scope. Start by cranking your elevation all the way to the top. Next, you are going to crank it all the way to the bottom, counting the number of clicks it takes to get there. Then crank it into the middle. Ex. if the number of clicks from top to bottom is 100, crank it up 50 (halfway). Repeat this for the windage. Mount the scope, or if it is already on your rifle, it's time to attach the boresighter.
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In a perfect world, the centre of your scope and boresighter would be in alignment. The reality is, they rarely are. If they were properly aligned, the small cross hairs indicating the centre would look like one in the pic below.
You want to get the boresighter lined up as close as you can to the scope. For this explanation, let's assume that the scope is perfectly parallel with, and properly aligned to the centre of the bore. Attach the collimator, which most people here call the boresighter. You want to get the two as close as you can to being perfectly aligned.
I use a magnetic boresighter, and gently attach it to the muzzle.. Then I hold a yardstick to the centreline (longitudinal axis) of the scope and centre my collimator to the line of the yardstick. Next, I look down on my rifle from the top, and align the yardstick so that it is centred along the longitudinal axis of the scope. I use the straight edge centre the collimator.
I look through the scope and make the adjustments to zero the scope's cross hairs with the collimator grid.
This always gets me on paper.
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Using a straight edge and a magnetic boresighter is a rough adjustment. The scope is not zeroed. When you read advertisements saying that the store is selling scoped rifles that have been boresighted, it really doesn't mean anything. Assuming that they performed the boresighting properly, you still have to zero the scope with your loads. And I would still check with my boresighter.