I prefer to zero the irons first. Then I dial the dot onto the top of the post, splitting the dot (half on top, half below). Then (with my AR's), I lower the BUIS and confirm the dots zero and fine tune it. When Im done, I bring the irons back up and check to see if they have changed, which they usually dont to much.
I have Ak's with Aimpoints on an Ultimak rail, and they are a lower 1/3 cowitness. Mr AR's are a center cowitness. With either, when I have my head down on the stock for shooting irons, the tip of the front sight pretty much splits the dot.