By default the pistol comes sighted in so that if you line up the 3 dots the point of impact should be on top of the middle dot's post. The replacement sights are just to change elevation if it's not sighted in correctly for some reason. You really shouldn't have to mess with it. Alternatley, if you spend time sighting it in to your personal preferance, it doesn't matter how you set up your sight picture as long as you do it the same way every time. I catch grief from my friends because they can't hit anything with my AR-15 but I can shoot an egg from 200 yards away, unsupported with irons so it's my sight picture that messes with them.
It is my belief that the 3 dots are for quick acquisition.
If you're wanting to shoot more precisely, you'll want to line up the top of the front sight with the top of the rear sight. Never mind the dots. Make sure that there's an equal amount of light on each side of the front sight post. Place your desired point of impact at the top of the front sight post. Be sure to focus your gaze only on the front sight, not the rear sight or the target.