Here's how I proceed. First, mount the bases in your usual way. Then, install the rings, using a hunk of 1" round stock to twist the front ring into line with the rear, while the side-to-side screws in the rear bases are turned in equally. Never use the scope as a lever for this purpose.
Lay the scope into the bottom half of the rings, squared up reasonably well. Be sure the adjustments on the scope are centered.
Bore sight, either with a collimator if you like the things, or by peering through the bore. If you need a big vertical change, remove the scope, shim the bases appropriately and repeat the above. If you need a big horizontal change, remove the scope, twiddle the screws in the rear base, realign the rings with the 1" round stock to bring the front ring around, put the scope back on the rings, and repeat.
Once the rings are bore sighted, ream or lap the rings into final alignment, install the scope so it is square, and finish sighting in using the scope's adjustments.
I'm sure there are refinements to this method, and likely somebody has a way of doing it better, but this works for me.
