At Baylor University, we use sub accounts, sub-sub accounts, and even sub-sub-sub accounts. 
Our three main sub-accounts are Courses, Organizations, and Manually-Created Courses. We use the latter for things like demo courses, template courses, or things that don't exactly fit within the official courses or organizations category. Under Organizations, we have sub accounts labeled Academic, Administrative, Athletic, and Residential. In these we create organization sites like departmental group sites, major-specific sites, residential community sites, etc. Finally, under the main Courses sub account (which is the only one loaded with data from our SIS), we have it broken down by school or college, and then by department.
It looks something like this visually (shortened tremendously of course):
Courses (structure loaded via SIS data)
- College of Arts and Sciences
- Art
- courses like Art 1301
- courses like Art 1302
- Biology
- Communication Studies
- Geology
- School of Business
- Finance
- Economics
- Management
- Law School
- Law School (some schools that are comprised of only a single department look something like this)
- School of Education
- Curriculum and Instruction
- Educational Administration
- Educational Psychology
Organizations (structure created manually)
- Academic
- organizations like Biology Majors
- organizations like Engineering Majors
- Administrative
- organizations like Biology Department Faculty
- organizations like Human Resources VP Search Committee
Manually-Created Courses (structure created manually)
- Demos
- Templates
- courses like NURSING 5342 Development Course
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