Mount the clamp in the same spots every time.
I only use one guide rod- which I have "adjusted" to be bent 90 degrees. I move it between the hones and lay both the rod and the hone on a flat surface (stone up) with the set screw loose to make sure they are aligned before cinching the set screw down. That should keep the geometry consistent enough through the entire process. That keep me from removing steel that doesn't need to be removed and concentrating on the job at hand.
Work one side of the edge for a set number of strokes, flip to the other side and repeat. The idea is to grind down until there's a thin 'wire' or burr of steel on the side of the edge not in contact with the stone and to work it back and forth until there's a sharp edge on the body of the knife.
When edge building with coarse stones, I work in groups of 50 strokes. Once the edge is established, I do 20-25 strokes on each side with a medium stone until I'm satisfied with the sharpness. Heavy use blades stop here. Fine and Extra-Fine hones are for refining or perfecting a fine, razor sharp edge that is overkill of rough use and usually too delicate for prolonged rough use.
Most knives don't need sharpening, they just need burnishing. When you use a blade, the microscopic edge bends to one side. Burnishing straightens the edge. For fine edges, I use a leather strop to burnish. Coarser edges get ran over by a chef's steel regularly. The direction of the burnish is immaterial. You straighten the edge just as well dragging the blade down the burnisher going away from the edge as you do going edge towards you.