Focus on raising discipline over grades and popularity. Public punishments, strict discipline, football practice. Also, be sure to go through Miss Potts's quest line to prevent losing a lot on her misbehaving class.
Yeah Ms. Potts' questline was the first one I went through too, because earning discipline back every day was a headache to deal with. Plus storywise, she has the worst discipline in class so it made sense to me to do that first.
