Oh me too, me too. Plenty to fill the digital bin, but the more you do it and the more you get to know your lens, the easier it will be. After a decade or so of using my old manual macro lens, I could put it down in front of my subject and it was usually bang on focus for whatever it was. I just knew its range and working distance so well it was second nature.
I have a two-part article about focus stacking (which I will be adding to with flash stacking soon) that starts with field practices and then moves to processing. You can find them linked in our longer stacking conversation, which I really should add to as I’ve found something in my camera I’d overlooked.