Hey Wayne,
Check out this link for how to use the alignment guide: Finding the Sweet Spot. The general rule of thumb for the depth key is to use the top holes for knives that are 1″ wide. The angle bar is calibrated for blades that extend 5/8″ above the top of the jaws. You can use the top holes on any knife, especially if you want to squeeze out a lower angle.
Having sharpened about 30 or so knives so far still leaves me early on in the learning curve. What are the rules or recommendation for using the depth and alignment key? I look at the knive data base and can’t figure out why some use the top and some use the bottom. I take it the you want the knive secured about the middle of the length but maybe there are other opinions. As always thank you in advance for all the great advise that everyone shares.