Since I have been out there in the field, masons approach things differently.
To answer the original question,
Use the shelf you have for the natural stone with the brick ties. Make sure you have a flashing system installed behind the paper on the wall, and over the stones concrete ledge.
Also Make sure your brick ties go over the paper you have installed, and are fastened to a stud behind the paper, they will pull out of the plywood.
Also install some weep holes at the bottom course, and try to make sure non of your mortar gets piled up behind the wall. Otherwise the weep holes get plugged from the back.
A scratch coat is only used with cultured thin stone, don't use it.It's a waste of time and material.
Here is a picture with brick.