It’s not Black Magic, but sometimes can seem that way.
The key to good honing, is understanding what you are seeing, and that can take some time to learn. Problem solving. A systematic approach, magnification and ink on the bevel, will help you greatly.
Remember, the goal is to get the bevels to meet, and then, get the edge as straight as possible. Once you are absolutely sure your bevel is fully set, joint it and reset it with light laps. It will straighten the edge dramatically and improve effects of your polishing and finishing stones.
You can straighten the edge, just by honing, but for the new honer, it is more difficult, because of the alteration of pressure. Jointing solves that problem easily.