When using square rule layout on hewn timbers, the framing square becomes more like a transit, you have to sight down the timber to be sure that you are square to the edge you're working with, rather than feel the edge as in sawn material.
I prefer to use lines on hewn material(and sawn material for that matter). I place level and plumb lines on the timber ends, then snap chaulk lines on the faces. If you don't want to see chalk lines on your timbers, you would need to either plane off the chalk after layout, or use a regular piece of string that is stretched over the face during layout.
Cutting is also different. In sawn material, you can more or less use the surface of the timber for the circular saw base/mortiser base, but in hewn stuff you will have to be more careful and sometimes use a shim with the mortiser.
I would be able to teach you what I know about hewing at one of the whippletree framing courses, if you'd like to visit Canada sometime....http://www.wpltree.ca/workshopindex.htm