Thanks for the links Jay.
This blog shows the process pretty well:
http://m.blog.daum.net/moksu080228/7718532.Establish a datum line on the posts, such as common distance down from plate joinery, and then find initial reference points on stones (such as one corner of post) and shoot elevations to see how far below the datum each of these points are. You'll then need to do a little figuring to establish the scriber settings based on the different elevations of the stones and the varying lengths of posts. Since the joinery is already done, you have one chance to get it right.
The March or June issue of Timber Framing had an article on this technique.
