Yes, you do move the rear sight in the direction you want the bullet to go (up =up), unless the rules of physics cease to exist in your world that should be what happens.
FWIW, I personally know competition shooters who have turned their rear sight adjustments the wrong way and ruined their day (I would like to deny that I ever have, but.....).
Usually it is from having your brain take a f(lapse) and you see the relationship of the carrier for the eyecup moving against the staff and an optical illusion takes place making you think you are doing it right, when you are not. Thats my story, and Im sticking to it........