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.
“The enemy is anybody who's going to get you killed, no matter which side he is on.”
― Joseph Heller, Catch-22