Basically, it's something you have to learn. Since RO calculates bullet drop, you have to take into account the distance between you and your target; the rifles are sighted so that a bullet will hit at the tip of the sight at a couple of hundred yards (I can't tell you exact numbers for each rifle). As you get farther and farther away from your target, the bullet will hit lower and lower on your iron sights. This is especially evident, as you said, in sniper rifles. Since you can see enemies at a much larger distance with a sniper rifle, you have to account for a much larger bullet drop.
Here's an example:
Let's just say for the sake of this that an MN 91/30 is zeroed at 200 yards, that is to say that if you were to fire at a target from 200 yards, your bullet would land very close to where the tip of your ironsight is. If you were to fire from, say 350 yards away you would have to aim higher to hit the same place than you would if you were shooting from 200 yards, since the bullet would have travelled farther and thusly dropped more over it's travel to the target. Therefore, if you were firing at someone with a sniper rife from, say 660 yards, you would have to account for quite a lot of bullet drop.
Basically all you can do is practice until you learn to just intuitively know how far away from an enemy you are and how much the bullet will drop in the distance. Either you're going to have to tolerate playing online and getting shot a lot while learning, or you can load up practice mode with some bota and take pot shots at them until you feel comfortable with your skill.