One of the easiest ways to ensure good alignment is to incorporate a jig cut or score in your project.
For example, if you want to engrave a logo on a cutting board.
First make a mockup of the cutting board in your vector art program. Place your logo on the mock up in the exact place you want to etch the logo. Make sure the mockup and the logo are different colors. This will allow you to toggle them on and off for later steps.
Second place a piece of paper on the crumb tray and secure it with magnets or masking tape.
Load up your .svg of the mockup and the logo into the GFUI. Set the logo to ignore and the mockup to manual cut 1% power, 500 speed, and focus .010". When you hit print the laser will draw/burn your mockup on the paper.
Without moving the paper, open the GF and place the cutting board directly inline with the mockup on the paper.
Go back to the GFUI. Without moving any of the objects set the mockup to ignore and the logo to your desired engrave settings (don’t forget to change your focus distance). When you hit print the laser will engrave the logo exactly where you want it.
I’ve personally used this technique to make board game minatures with front and back engravings. It works very well.
I find ikea mala drawing paper works well for this technique. It’s inexpensive and is wide enough to cover the entire cut zone of the laser. You can get about 58 jigs out of a single roll.
When I first got my GF I had similar questions about alignment. Everyone one very helpful. I did some experiments trying to map the error you can look at the thread here: