I will try to explain the square rule my self as best as possible:The Term "Square Rule was Coined to Edward Shawn in the 1830s in one of his books. Its based on the idea that within every irregular, rough sawn timber lies a slightly smaller perfect timber. All joinery is cut to this inner timber, which usually shares two adjacent square faces.
This way it does not matter if all the timbers are different, you have two lay out faces that you measure from to do your layout.
The steps for laying out are easy:
1. Make sure your primary face is flat, than make sure that your secondary face is flat as well and square to your primary face.
2. Layout all your joinery from your primary face / Layout face.
3. Draw your joinery on all surfaces including the other non layout faces.
4. Cut according to your layout and hope it is all right!
Using a jig that helps me a 45 Degree angle I start Chiseling my way trough the wood.
By the end this is what it should be looking like. The rafter will be sitting on there, it will be nice and strong.
Using a chain mortiser you can cut a Mortise in a a couple of minutes. Have your layout ready, set up your Chain mortiser by placing it on and locking it in place, set it to the right depth and than start drilling /cutting!