I hope some of what follows will be helpful.
From your description, I am assuming that you are working with relatively straight logs and that the members will be at 90 deg. to each other. The joint you are trying to layout and cut sounds like a fully housed M&T with the bottom of the housing being the bearing part of the joint. The starting point is to layout plumb and level lines through the log center at each end of the log and snap the lines on the surface of the log. These will serve as your reference for all layout work. Parallel plumb lines on the ends will mark the tenon or mortise width and you can chalk them on the face as you did for the log center lines.
To layout the tenon shoulder, start by marking the shoulder point on one of the reference centerlines. From here........flexible straight edges are a must. I use japanese framing squares for this because they are flexible. Lay a square along the centerline reference with the tail side aligned with your shoulder mark. Tack this square in place with small flathead brads each side of the square. On an adjacent reference centerline, tack another square in place with the tail side touching the shoulder side of the previous square. You now have a reference square..........bend the squares down towards the
log and mark several points on the log along the face of the squares. Do this same procedure around the entire log so that when finished you have marked points around the entire log that will form the line of your tenon shoulder. Connect the dots around the log and you have a shoulder line that is perpendicular to the log center line. To do this I use salvaged pieces of metal banding. The kind that comes off of lumber bundles works quite well since it is long and straight. Wrap it around the log, connecting the dots, and mark your shoulder line. Depending on the accuracy of the tenon faces you can, as you are doing, use the tenon as a reference for checking square on the shoulder.
Using this layout method you can also layout the mortise on the other side of the joint. Layout and cut the mortise first and then mark and cut the housing for bearing. To mark the housing around the mortise you will be scribing the profile of the log on the tenon side to the log on the mortise side. Trial assemble the joint and hold the tenon shoulder back an inch or so from the face of the mortise log. Make sure the logs are square to each other by checking centerlines on the faces. On the bottom of the tenon log.......mark the depth of bearing you want along the centerline using the tenon shoulder as reference. Using a double pencil/pen scriber, set the width of the pencils from face of
mortise log to the bearing depth point. Proceed to scribe the profile of the tenon log onto the mortise log all around. Score the line just marked on the mortise log and remove the housing material to the depth of bearing. I've learned that good scribing is an art that requires much practice.
I hope this brief description helps. If nothing else it will give you a starting point to work from. Methods and techniques vary from person to person so ask around for pointers. Good Luck!
