This is an interesting discussion. Mike uses the long edge of the brace as the reference. I usually use the short edge. This results in a variation in how much "reveal" you get on the brace's small plumb and level faces. But it lets you determine the length of the mortise on the other stick, since the shoulder length on all the braces will be the same. You don't need to cut it extra-long to account for the worst-case brace size.
Edit: Forum shrunk my picture. If you load it from the source, it's more legible.
