Hi Stephen. Welcome to Moodle. Don't worry, it takes some time to sort everything out so be patient. Also, remember, it's almost impossible to break Moodle so you can experiment!
OK. To your question. There are some compulsory courses and some elective ones? I think the answer depends on how you want the students to look at them. For example, there's much to be said of having all the courses on one page e.g. topic view. That way students can view/taste the courses before they join in. If you grade activities within the courses then gradebook will have some empty cells depending on what is completed but you'll still get a score (more advanced calculations would need you to ensure cells aren't part of the score - empty = 0 etc.).
If it's a case of sorting students out prior to the course and then allowing them to see only certain parts then groups and grouping is the way to go.
I always get my students to help me design the site. They get and input and feel ownership over what gets put up. Why not ask yours?
Teaching with Moodle
Course - Different Subjects - Some Core - Some Electives
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