I don't know that this will help, but I can describe the way our site is set up using categories.Our site has three main categories (Schools, Central Office, Help/Resources), with further sub-categories from there.
Schools, for instance, contains the categories Elementary Schools, Middle Schools, and High Schools.
The High Schools category contains a separate category for each high school (14).
Each school's category contains a category for each major discipline, clubs, faculty resources, etc.
individual courses are housed in these last categories, so a high school biology class might be in Site > High Schools > ABC High School > Science > AP Biology - Smith.
This structure sort of evolved pretty quickly as we started using Moodle several years ago. It seems to work well for our students - they click through a path that is analogous to going to their school, finding the correct hall, then entering a specific class. After enrolling, the Dashboard makes it easy for a student to return to a course. Looking back, I'm sure that it could be much better. One example - we have around 50 elementary schools, so there are that many categories in the site named "Fourth Grade".
I haven't done much with cohorts, but I do add everyone with a teacher email address and the teacher role in any course to a cohort that is enrolled in a support course - and then use that support course's Announcements forum for system notices.