If you have ever used another database program, it helps to think of iTunes as a database manager, which it is, and not worry so much about what the underlying file structure is, because you will never have to look at it if you don't want.
Within iTunes, you can set any file to a particular Genre through the Get Info menu (right-click on a file) Under the Info tab. This can also be done using a program like Subler or MetaX (or Z. whatever it is now). It won't change the file structure, but you can ignore that. If you go, within iTunes, to the Grid display, you can then choose to see the films by Genre. Then you open into any Genre folder within iTunes, and see all the files within that Genre, change their names, add then to a device, watch them, whatever you wish Meanwhile, you're letting iTunes worry about what folder they happen to be stored in, so you don't have to.