I hate V-notches for this very reason. But, you always leave the top of the front sight even with the top of the rear sight, regardless of shape. I take a jeweler's file and file the notch square, then open it up to give me daylight on both sides of the front sight, equal to the width of the front sight as seen thru the notch. That allows my eyes fo focus on the front sight, and still center the front sight in the rear sight notch.
Now, if you are engaging in " kentucky " "elevation" or "windage", you will either lower that front sight or raise it above the top level of the rear sight, depending on where you have zeroed the sights with a given load, and the distance to your target.