Why? The easier navigation is for students, the quicker they get to the content and activities and experience less frustration. First, keep your navigation relatively simple. Second, keep it very consistent. Third, use visual clues to help the user. Fortunately, most online courses are organized into classes or modules so you already have an organizational structure. Within each of these sections, spend some time analyzing your materials to develop a consistent sub-set of folders to house all materials. If you use the same sub-set of folders within each class, students will begin to expect the similar materials to be housed in the same location throughout the course.
Did you Know? The best organized courses look so simple that anyone could navigate the course. This is exactly what you are seeking. Consistent organization (called internal standardization) assists users to anticipate where they should go next and what they will find when they get there. Using some visual indicator (usually an image with an alt tag so it can be read by a screen reader) helps users to quickly see the organizational categories.