For the range you're shooting, I'd suggest either a 100-yard zero or a 50 yard zero.
With a 50-yard zero you'll get a flat trajectory from 50 to 225 yards... within this range your bullet will impact no more than approximately 2" high. This allows you to shoot dead-on for most targets without worrying about holding over/under.
With a 100-yard zero you'll get a flat trajectory from around 25 to 200 yards... within this range your bullet will impact no more than approximately 2" low. Same thing as above... just shoot dead on within this range (unless you're hunting small game).
A 25 yard zero is not a good idea at all (and will not recross your zero mark at 200 yards as someone said above). At the bullet's apex it's nearly 10" high, meaning it is NOT flat shooting in the least. It doesn't re-cross the zero mark until the 350-yard mark or so.
As for the sights, IF your large & small apetures are on the same plane, then zero in with the smallest for the best precision and you're good-to-go for both. However, it's possible your small & large apetures are not on the same plane, which means your zero will shift when you switch between them. At the ranges you mention, I think the small aperture would be your best bet. Then you can test w/ the large aperture to see if your zero changes. If it does, take note of the difference and use the sight accordingly. The large aperture is really only useful for real close-up work, which is the reason some sights incorporate a POI shift between apetures.