I keep boxes that have larger flat surfaces and slice them down to fit on the honeycomb or I keep packaging cardboard separators. We got a large shipment of books at work that had a 10 x 12 sheet of cardboard in between each book. I have a slew of them for small projects. Use the hold down pins that have been posted here or some strong magnets.
Discussion of settings belongs in beyond the manual. We can move this topic to that category and go to down on settings and the like. It doesn’t seem you have a real problem with the machine, just learning how to adjust calibration and setting focus.