I went to the range the other day to implement the IBZ (Bushmaster 20", 1/9, Q3131a ammo) and discovered a peculiarity... After zeroing with the small aperture at 50 yards (3/8 minus 2 clicks) I switched to the large ring and and clicked up twice (to 3/8). According to the procedure this should shoot to the same spot. However, I had to go an additional click (3/8 + 1) in order to do that. My question is, should I re-do the process starting with small @ minus three clicks or will that hose the long range calibration of the small aperture? I prefer using the large ring for short range, and because I'm sorta anal I'd like to have it be "on" at the 3/8 position (less to remember). On the other hand, when I need the small aperture it would be nice if it were accurate as well.
Any knowledgable comments/ideas?

what is your ultimate goal?
sounds like you were hitting dead on at 50 with the small and a little low with the large.  fire at 200 to be sure of your battle zero and adjust for the small to hit at 200.  then go back to 50 and fire to verify the large "is close".