I never use the markings on my mat. I hold down my ruler with my left hand and rotary cut with my right hand, on the right of the ruler to get a straight edge. Then I rotate the matt and measure from the straightened edge to cut my sub units on the right. Can you tell by how many times I've said "to the right" that I am very right handed and left hand challenged? Go figure, two of my sisters are left handed.
Looks like a real nice mat and I hope you can make it work for you. The marker sounds like a good solution. Quilters are pretty ingenious!