Visual aid...
get a pencil, pen, ruler, or other straight object, and hold it up ionfront of you. Imagine this is your line of sight. Aim at your target (or a representation of it) Aim at center. Now, holding the pencil at the back end (closest to you), which way to you move the front of the pencil, to point at the bullet holes?
Thats the way you move the crosshairs in your scope.
The same method works for iron sights as well, but the process is just opposite. For Iron sights, hold the pencil at the front (representing your front sight) and move the back until your line of sight matches the bullet holes. THis is the way you move the rear sight. Note that the direction of movement of the rear iron sight is just opposite the direction of movement of the scope crosshairs! That is because of the single focal plane of the scope. IT sounds odd, but try it, it does work.