I have A2 sights on my Bushmaster. I know the 0-2 aperature is intending for 0 to 200 meters and the other smaller (unmarked) aperature is for 300 plus meter shots. The question is if you use the smaller aperature at distances less than 200 meters, will that affect your accuracy?  

Yes. IIRC, using the small aperature will generally cause the bullet to impact lower than with the large aperature.

It will affect your speed in aquiring a target more than anything (though once aquired it will be more precise). At distances less than 200 meters the bullet will only cover an average of 5". Half of that 5" will be below your sights, the other half above (arc of the bullet).

What is IIRC?  

If I Recall Correctly.

The larger aperture is best used for close ranges, true. It also is useful in limited visibility and for snap engagements or moving targets. Consider the 0-2 to mean that it should not be used PAST 200 meters, not that it is the only sight for use within such close ranges.

If your weapon is zeroed for 300 meters, you will be shooting high at some closer ranges, but not enough to seriously throw you off target. I would argue that your bigger concern would be to have a target appear at longer range and have trouble engaging it because of the larger aperture. Believe me, it is VERY difficult to angage longer range targets with that big aperture and it does throw off your zero as gregw45 indicated.

Adam