Hi! Welcome to the fun house!
With the tray in you are limited to half inch thickness, with the tray out you have right at two inches. The thing is the surface you want to engrave has to be within 1/2 inch of the head to be in range of the focus.
@dwardio devised This helpful tool and shared it with the community. I find it very useful, and easy to check the material height.
I have found that scraps of 3/4", 1/2", 1/4", and 1/8" boards work well for shimming up your work with the tray out to get within the range of focus indicated on the ruler. 