There are several steps that folk might slide past that they need not to. first among those is Calibration. The camera is a “fisheye” and calibration does the math so it approaches actual x-y locations for your machine.
Set Focus will match that math to a specific location creating the math to match best there, and measure the height of the material at that point. then where you move the design image will match what you see on the crumb tray. With the image highlighted you will see a widget in the lower right that when you pick it shows the precise size and location of what you have highlighted. If you record that information, you can place anything at that location and it will cut there no matter what the design image is showing.
If you make some Bed Pins you can establish a precise location that you can place pieces repeatably at that precise location 