Your pins should be centered inside of your pin guard, however, how will you adjust for trajectory while just centering your pin guard? To me it makes more sense to center the pin you plan on using. By keeping your pin guard centered all of your shots would hit the same spot no matter which pin you are looking at. I am only talking about multiple pin sights.

If you are using an adjustable, single pin sight with the pin centered in the housing, you will have no trouble with trajectory because you are raising or lowering the whole sight thus being able to keep the pin and the housing centered. With the multiple pin sight you will only be able to keep either the housing centered or the pin, not both. (Unless one of your pins is located in the center of the housing) In effect, this is the only pin you'll be using by centering the housing. With that, I don't know how you can accurately gauge your trajectory by only centering your housing.