If the top of the disks is sitting 1.5" below the camera, there is no way on earth that the beam is going to be able to focus on it. So i’m not surprised that you are having alignment issues with those.
If you are cutting without the crumb tray, you have to prop the material up so that it falls into the correct engraving zone. The engraving zone is about half an inch from the top of the crumb tray down to where the surface of the crumb tray would be if it were in there.
Trying to engrave on an unsupported item is probably why the alignment is so far off on your lids.
The other thing that you have to do every time you try to engrave without the crumb tray is correctly calculate the “Thickness” of the material and enter it into the Unknown Materials slot. I have that highlighted because it’s not the actual thickness of the material that you will enter in this case, it is the thickness of the material that extends above approximately 1.4" as measured from the metal plate on the bottom of the machine.
The honeycomb surface of the tray is considered the zero point for focusing calculations. The laser can only focus correctly in the half inch range that runs from the top of the honeycomb and half an inch higher than that. So you prop the material up so that the top surface falls into that range, then subtract out 1.4" to get the correct thickness value for the Unknown Materials slot in the Thumbnail column.
There are a couple of very good tutorials here that explain what you have to do:
That’s part one.
The second issue that folks are trying to help you with has to do with achieving perfect alignment through use of a jig, instead of just trying to eyeball it. It is more accurate (100%) and taking the time to do it is going to be a real time saver for you if you have a lot of the same shape to engrave on…you just cut one jig hole, drop each lid into it, and engrave it perfectly. But it’s harder to do without the tray in place, you would need to prop the jig up as well. Maybe a small sheet of plywood propped up on scrap wood. As long as you do not move the jig or any of the images on the screen, it will engrave in the correct place.
But look at the tutorials for cutting without the crumb tray first…I think that might be the main problem here. You might get good enough results once you get the material into the correct range with the correct thickness listed to not have to mess with a jig.