If you include the engraving in the original file that you used to cut the grid, the alignment will be perfect without having to place the engraves using the camera.
I realize it’s a little late for that sheet of plywood, but it’s probably going to be worth it to rework it.
You would place your engravings relative to the cuts in the grid, set the engraves to Ignore, cut the boxes, put the little things into the holes, and then run the engraves. (Turning off the cuts the second time.) Make sure you tape the backing piece down so it does not move at all.
(Oh, and elevate the plywood sheet so the surface of the sheet is at a level with the top of the things - you will want to drop the things down into the holes and not change the focal height by too much.)