Bryson:

Scribe rule is just like the process trim carpenters go through when fitting a base board or crown moulding.

The timbers are aligned as they are expected to mate in two dimensions (generally in plan) and offset in the third dimension(elevation). You could think of this as a virtual assembly. Then, the the joinery is created on one piece and its outline is transferred to the mating piece with scribes, calipers or plumb bobs. Generally, the process it to cut the first half of the joint on one piece and then transfer the outline to the mating piece. The first half is usually the tenon and the second the mortise because it is easier to project the outlines from the tenon to the mortise rather than vice versa.

Before the advent of sawmills, entire structures were created this way from crooked timbers (AKA the cruck frame). In the French scribe method, the timbers are drawn full-scale as mated on a level surface below the timbers and then the joinery and alignment is projected up on to timbers with a special plumb bob with a built-in cross hair.

Good luck.