You will find this a challenge.
Taking a first view, of considering separating the CONTENT (Here is a video on newton's Law) and INTERACTION (ask any questions here about assignment 1) and PASTORAL CARE (Mr smith is away today)
I've been in situations where we set up courses like this, and what happens? maverick teachers just start teaching in tbeir own space with their own resources, and collaboration/sharing of resources goes down the tube.
The basic challenge is that Moodle 2 allows sharing of file resources between courses, but nothing else. You can't share for example a section. So you are left with solcing the membership problem with groups or extra courses.
A combination of groups and cohorts will work, but again here you have a time consuming pathway to set things up. Check out: there is a new grouping option in 2.5 http://docs.moodle.org/25/en/Import_groups Moodle at the moment is easy to set up, but requires a lot of clicks, and long workflows to get where you want/
My current favorite way to work: home course (for my class) links at the section level to other subjects. This in theory only needs two types of courses: 9NY physics (HOME) and 9Physics subjects (SUBJECT).
- create a label in HOME courses with the course outline in time order with links to SUBJECT. Maybe a calendar reminders. This then follows the rule of one: courses organised from ONE place, you don't have three places to go for the outline.
- Or have several labels to do the same purpose.
Think of pilot soon.
Sorry for slightly disjointed post, best I can do before going out for a day of painting windows.
Added PS: I think Moodle navigation may be a bit stressed with what you are proposing.
We use a plugin (course menu) and the Awesome Bar. See http://docs.moodle.org/25/en/Decaf_theme#Illustration_of_decaf-course_menu_combo for a picture. This gives a nice little course menu and easy navigation between sections.