Hi @MattJKelly
The way I think about it is that the "course" (shell) is where all the course materials, assessments, student work, grades, etc. are stored. The "section" is where the enrollments connect to the users.
In Canvas, each course shell has its own "default" section, but you can specifically create one or more sections within a course using SIS integration, and specifically enroll students in a particular section, rather than a particular course.
You can also "cross list" a section, which means that you are moving the section from one course shell to another.
The benefit of enrolling students in a specific section rather than a specific course in your SIS integration is that if you choose to cross-list a section, the enrollment feed for your SIS integration does not need to change.
Students can be enrolled in more than one section that is cross-listed into the same course shell, or they can be removed from one section and added to another section within the same course shell, and their course work, grades, etc. are all preserved.
However, if you remove the student from a section that is in one course shell, and add them to a section that is in a different course shell (or, alternatively, if you choose to cross-list a section to move it from one course shell to another), then any course work, grades, etc. from the first course shell will be lost. That is why we do not allow instructors to cross-list their courses after the semester has started....