First, secure the gun in a cradle and remove the gun's bolt so you can see the bore. Line up your barrel on a spot 25 yards away. Then adjust your scope so it's sighted in on that same spot. Make sure the rifle doesn't move and be sure to recheck the alignment. When using a bore-sighting tool the process is much the same except you won’t remove the bolt from the gun and will adjust the scope to align with the tool.
You should start at 25 yards for the best chance to land your shots on the target paper. Pick a steady bench and use sandbags or a shooting rest to support your rifle. Looking through your scope, aim at the center of a target, and shoot two shots at one spot on the target. Measure the distance from where you thought you were shooting (point of aim) to the center of the group of shots (point of impact).
Adjust your scope so the point of aim is moved to the center of the group. Shoot two more shots and you should find your point of impact is very close to your point of aim. To sight in for other distances, repeat the same procedure at that distance.