Some good info on sights and sighting in your AR.
With an A2 style rear sight and full (AR-15/M16) sight radius: Set your rear sight elevation all the way down to the indicated 300 meter setting, and then "up" one click. Using your unmarked (small) aperture, adjust only the front sight and the rear windage (leaving the rear elevation at one click up from 300 meters) to center your five-shot groups exactly at point of aim at 25 meters (about 27.5 yards). Return the elevation knob to an indicated 300 meters. You are now supposedly zeroed at 300 meters when using the small aperture (read on). The large aperture is intended for use from zero to 200 meters when the rear elevation is set to 300 meters. (For the M4 type weapons, follow these instructions, but do your 25 meter zeroing with the rear sight set two clicks "up" from the 300 meter setting.) Military instructions tell us that you are now done, and your point of impact corresponds to point of aim at the indicated distances when firing standard ammunition, all the way out to 600 or 800 meters.
We will consider this your "rough zero" however. Remember that at 25 meters, any small error (either in your point of impact or in your individual rifle's muzzle velocity) will translate to a much larger error at 300 meters. Any error at 300 will be at least twice as large at 600, etc. For the precision marksman, start with the above 25 meter procedure, then shoot at a much longer distance and fine tune your zero. Set your rear elevation wheel to, say, 500 meters for example, and shoot for zero at a measured 500 meters, adjusting only the front sight and rear windage, on a windless day. Any small errors in your system will have thus been minimized for 500 meters, and will be negligible at shorter distances, assuming standard ammo.
One good method, providing you have the necessary time and ammo, is to start with your 25 meter zero, then move out to 300 meters, 300, 400, 500, and so on. When you're dialed in at long range, your front sight is better calibrated to the rear sight's range settings and you can have more confidence in your weapon. You can now work back through the shorter distances in 50 or 25 meter increments, taking notes of where to set your rear sight for precision shooting at various odd distances. One or two good days of this and your confidence, skill, and knowledge of your and your rifle's capabilities will have been significantly improved.
If you're using non-standard ammo, or if your rear sight's range settings aren't factory-calibrated for your barrel length (16" barrel with M4 sights for example) your elevation settings will be a matter for some more experimentation. Time spent working out the bugs at the range will help improve your shooting skills as well as your knowledge of your rifle.