Technically this has nothing to do with Media Manager other than perhaps a cosmetic resemblance of how you might want things to look after your customizations have been completed.
If you want to have security control over who can download what, you'll have to revamp the download infrastructure. Simply moving media folders around isn't going to accomplish anything other than error messages.
To arrange downloadable files into groups, you'll need to:
- alter the database infrastructure to track the grouping arrangements
- write an admin interface to allow you to set the grouping arrangements
- rewrite the download templates to display the files in the prescribed groups
- rewrite the download logic accordingly
- revamp the system to allow you to add additional files to an order's downloads after-the-fact
- and so on



