hello John:
here is a topic that really interests me, and one that I am quite familiar with.
Working with and doing layout on hewn timbers is a time consuming and skill testing proceedure. It also requires a fair amount of perseverence even by someone that is already a good tradesman in another facet of timberwork.
One of the first requirements is to work very accurately, and by this I mean every move is dedicated to as near perfection as possible, if you strive for this you will not have any problem turning a rough hewn surface into one with motises that will accept tenons and seat out nicely.
I suggest putting only one main chalk line on each of the four surfaces using a fairly fine grade of line for this purpose. Before you start to put on reference lines though I suggest that your work horses\supports are placed fairly level to one another, and then placing the timber on top with the outside surface facing up. Check the timber for wind, and if wind is evident with shims\wedges split the wind so an equal amount is shared by both of the timber's ends. You are then ready to strike a plumb mark on both ends usually 4-1\4" from the outside of the timber, using a level and a sharp scratch awl. When you eventually strike a chalk line from end to end on both upper and lower surfaces, this line will be along the inside of all the mortises, and should be accurate providing that you take precautions to snap the line accurately. The next step using a square on the ends again laying the blade along the vertical scratch mark, and down again 4-1\4" from the upper surface scratch cross marks on both ends. Complete your chalk lining on all 4 surfaces, and you are ready to do layout of mortises along these lines. At this point you are just getting started nicely, and you should have a good understanding of the measurements and location of all mortises their orientation on each timber, what braces are involved. Always remember and place the timbers in the same orientation order before beginning work on each one. I usually number each timber and record it on a work sheet for referral, you will need this important information eventually for assembly. I use dummy tenons to test the mortises as I work along, and feeler guages made of 1" pine to slip over the tenons as they are cut out and shaped.
Good luck, and have fun, I am here if you need further help or advice, I am sure that others will also, there are many good framers out there
the NH