There are many ways to mark and cut notches - except that I do not cut notches
I cut the notch in on the pattern.
I cut straight across the fabric, straight across the notch.
I mark the fabric with permanent marker right in the middle of the pattern's indented notch.
Here are some examples of notches I've used. I try to mark the fabric with a pen color that will contrast with the fabric.
Most pictures will get bigger when you click them:
Have you tried this method with pattern notches?
Do you have a special trick for notches?