Students are enroled in a single Form/Roll Group, under People > Students > Manage Student Enrolment. The teacher(s) of this form group are then associated to the student. This would be the main person/people in school who are responsible for the overall development of that student.
Students can be enroled in as manage classes as desired, under Admin > Timetable Admin > Course Enrolment by Class or Course Enrolment by Person. Teachers can be assigned to these classes, and the class placed in a timetable. This forms the subject teaching part of the school.
Of course, you can use Gibbon in any way you want, but feel free to use these as a starting point.