The categories in the add edit courses screen are ordered by id number of the category, so are the sub-categories. There should be an option much like the courses to order the categories or sub-categories within a category.
Example:
Category1 (id=4)
BSubCat3 (id=9)
CSubCat1 (id=8)
ASubCat2 (id=7)

Allow a option to order to show like
Category1 (id=4)
ASubCat2 (id=7)
BSubCat3 (id=9)
CSubCat1 (id=8)

I am will aware there are arrows to move this the way you want but its not friendly to do that when you have to reorder 100s of categories and courses.