One thing I have noted is that when I am trying for a very deep engrave, I sacrifice time to lessen charring by going over in multiple passes to get to a depth I need.
Although it is buried in a long post, in the design file I have two squares that I have set up that I can use for testing depth engraving. Since I need it to be 1/2 depth engrave and that can vary with materials, I usually test with these small squares. Then I can match them up and see how flush they are.