Scott, I have a Facetron. The use of a cheater adjustment is invaluable for you to level your table and get it to meet adjacent facets. First off you need to have the machine itself zeroed out before you ever begin. Install the 45° adapter that you would use to cut and polish the table and lay it down on a clean polishing lap or master lap with the machine set at 45° and a 96/0 index (zero I dex on whatever gear you are using). You will have to raise or lower the quill with the fine adjustment so that the adapter is JUST sitting on the lap (I have a ceramic lap I like to use, because it is solid and absolutely flat). The cheater should be set at EXACTLY zero. I even make a tiny mark on the silver dial right next to the tick mark on the anodized area to the right so you can see them line up just that much better. Also, make note that the grooved piece of metal that points to the index mark (say the 96 mark on a 96 gear) is centered in the channel is rests in. There should be an equal amount of space on each side; about 1/8″ or so.
If you can slip a piece of paper (find some sheet of fine grained paper like a glossy magazine or smooth office paper to use as a shim stock or an actual piece of shim if you have one), your cheater is not zeroed. Don’t move the cheater, make the adjustment with the star nut that holds the index gear in place. You need an Allen wrench for this. Loosten the nut and the adapter will twist left and right. What satisfied, tighted the nut. Take a really long time making sure this is as accurate as you can do it.
When you next go to cut a new stone, if your machine is zeroed perfectly, when you start cutting your girdle, you shouldn’t have to adjust your girdle at all for all facets to line up as you go round (meaning to use the cheater). Depending on your level of skill and equipment (power eye loupe, head visor or microscope), as you do this each facet will be microscopically a little higher or lower than it should be but do your very best to line up each corner one at a time.
The art of gemstone cutting reflects the skill of the faceter to line up not only the girdle facets but all others until you finally get to the table. It is pretty much impossible to get to the point of cutting and polishing the table and not have to use the cheater because of the microscopic faults in lining up all your previous facets. It’s just a part of the process that you need to master but if your machine was properly zeroed from the beginning and you’ve been attentive to lining every facet up pretty well, the amount of cheating should be kept to a minimum. You should not be able to visually see that a table (that is supposed to be level by design) is tilted: ever. But our vision typically is not good enough to see minor cheats.
The cheater on the Facetron machines are marked 0-7. With your stone in the adapter, pivot the quill uptight to inspect the table. As you pointed out marking the stone with Sharpie markers before you cut or polish will let you see where the grinding of the stone is actually taking place. If you find that you have to tilt the stone so that it cuts/polishes a little more on the left, adjust the silver cheater -‘downward’ so that you are going from the zero mark down to seven or so. Maybe more or less, you have to figure out how much.
If you need to cut more to the right, you ‘go up’, meaning your adjustment would go from zero to one. If you need to shave more off the top or bottom of the stone that is the height adjustment and not the cheater. Mastering the cheater takes some time but is critical to improving your abilities.