When installing a scope, I first set the scope windage and elevation adjustments at mid point. Then I install the scope and use the elevation adjustment on the rear ring to bore sight it (on a Remington 700 or 798, for example, which have this feature).
A shim is sometimes needed under the scope in either the front or rear ring to get the elevation adjusted.
In this way you get the best optical image from your scope. The windage and elevation adjustments should only be used for minor corrections when you sight in your rifle.
I have found that poor accuracy usually results if scope installation isn't done this way. Significant optical distortion sets in the further you get away from the mid point windage or elevation settings.
On rifles that don't have the windage adjustment on the rear ring (Ruger, or rifles that use a Weaver-style base and rings), and there is significant lateral misalignment between the mount and the barrel then you've got trouble.
On these rifles, shims can be installed under the scope to correct vertical misalignment, but shims can't be installed to correct lateral misalignment. I have had to use Burris Pos-align rings with offset inserts to correct lateral misalignment on these rifles.