If you zero with the small aperture, your point of impact will change when you flip back to the large aperture (you will be low). If you zero with the large aperture, your point of impact will change when you flip to the small aperture (you will be high). The only way around this is to replace the ARMS #40 aperture with a same-plane aperture.
Alternatively, you can do what I've done and zero the small aperture at 50yds. At close ranges, I am a low with the larger aperture and holdover at extremely close ranges is even higher; but at those ranges, being off a little is less important. As distance increases, so does time to flip to the small aperture for better accuracy. From 50-225, I am within 2" of the point of aim and using the notch, I can hit out to 500yds on an IDPA silhouette.