How is everyone zeroing their 9mm upper? I was using the Santose method, but it doesn't say anything about if I should be using the 300 m site and go one click up or should I just use the 200 meter site? Also, I got my windage set up and it is 15 clicks to the right... is that excessive and would you recommend sending it back to Olympic arms?

I had a friend set my to battle zero.... what ever a 223 is set to.

It acutally shoots 6" or so high at 25yds.  At 200 it shoots just about point of aim (give or take).  Takes a while to get there, but it does....

I zeroed the wifes at about 45-50 yards. Left the rear elevation in the bottom 300m setting. Hits almost POA at 15 yards all the way out to 50. Havent tried past that range yet. Was very impressed with how flat shooting it was. Use your small peep app on the rear to zero. There is no different in POI with the small vs large. The small is used for longer ranges because it gives a more precise sight pic. The large gives you a better field of view, thus its use from 0 - 250/300 meters. Cant use the elevation adjustments on the rear accurately anyway with it being a carbine, and a 9mm at that, so just leave it set all the way down.

300m - With a 9mm?

My 635 is zeroed @ 50yrds, and no problem with 100yrd targets.

After reading the charts again, I guess it really comes down to where you will be shooting. I think the 50 yard zero is better for a CQB/Urban environment and the 25 yard zero is definitely better if you plan on getting out to 100 yards. For my wife, her 9mm Oly is going to be a close range gun. Probably wont ever need to engange out past 75 yards. The 50 yard zero seems to be a bit flatter out to the 50 yard mark, which would explain our experience so far. Again, depends on how you plan to use the gun.

I zeroed my Colt 9mm exactly like that article you linked to. The guy give a clear explanation as to why the 25 yard zero is better than a 50 yard zero and it makes sense to me. Basically, with a 25 yard zero, you obtain a zero out somewhere around 80 yards. At 100 yards you are down 1.1 inches. So, with the 25 yard zero, your bullet will be above your line of sight the whole time. With a 50 yard zero, your bullet is below your line of sight everywhere except 50 yards.
I am not sure what you are talking about with the 200 and 300 meter sights. On my Colt one leaf is marked 50 meters (the sights are similar to A1 sights). That is the sight leaf I use. FWIW, my rear sight is adjusted way over to the right on  all my ARs.