"Months in Use" should be the count of months that your school is in session with all your students and teachers. You shouldn't include the summer months when school is not in session, unless your school is open for camp or summer school. "Months in Use" is only used to determine your eligibility for ENERGY STAR Certification (minimum requirement is 8 Months in Use).
Occupancy should be the percentage of your school that is occupied when school is in session.
Neither Occupancy nor Months in Use impact any of your metrics, including your score.