Multiple menus by post categories and sub-categories

Hello everybody

I’m working on an educational site, containing a set of articles, which should be ordered into the following hierarchy:
course (ex. ‘biology’) -> sup-topic (ex. ‘genetics’) -> article (ex. ‘The DNA-molecule’)

I want the main menu to reflect the top level (course), which is easy enough, as it just requires a custom menu, displaying my categories.
The problem is, that I want a sidebar-menu to reflect the next level (sup-topic), under which the articles should be listed in the menu. The image in the link below, should show what I mean:
https://i49.tinypic.com/2uyixbc.png

How do I accomplish that?
I don’t want the user to be brought to the typical categories.php, with a list of posts in that category. The categories are only for structuring the menus and the hierarchy of the site.
If categories aren’t the best way to structure the site, I would like to know as well ??

I hope someone will take the time to help ??