As far as storing it in two variables, I use one called Alignment. And if you get bad points you subtract from it, and if you get good points you add to it. This way it can track your alignment without confusion. As far as displaying it in the menu, I would love to know how to do that, lol. I just use this one person who changes depending on your alignment, the more evil you are the more demonic he looks, the more holy you are the more angelic he looks.
You can manipulate variables in the... first tab on the events list. there you can add, subtract, set, multiply, divide, module your variable. So whenever he does whatever he does to get bad points, you just use the event control variable and subtract x from the variable that is his alignment. Is that what you were asking?