I figured someone would mention this but no one has, so...
The mil-spec AR-15 apertures, large and small, are not on the same plane. The larger is for shots from 0-200 meters and is for faster acquisition and/or moving targets at close range. It is used all the way "down" in the adjustment range or when the the 3 is aligned with the mark on the left side of the receiver. The smaller aperture is for 300 meters and farther, I believe. When you shift from one to the other, there is an elevation change that needs to be taken into account.
This is one reason that "same plane apertures" have become very popular. Many companies make them and a quick google search will turn up tons of info. This is not what was originally intended, but it allows the shooter to swap back and forth without experiencing the elevation change so the same zero can be used.
There is some good info on zeroing an AR based on the military methods here:
http://ar15zeroing.com/
I have to admit, you guys are making me want to put the irons back on my AR. I used to really enjoy shooting with them, but after seeing the advantage of a low power optic in 3-gun or multigun competition, I haven't gone back...