WordPress multisite has some restrictions regarding folders in a child site mapped to a separate domain.
That said, If you want to create folders in child sites, you can do so.
You could add a directory/file directly into WordPress installation root folder and that directory will be available as "child-site.com/some-folder".
You could also add subfolders like "child-site.com/some-folder/2-level/3-level" and they will also work fine.
The problem is the same folder will be also available for all sites on the network, for example as "another-child-site.com/some-folder".
This is usually not a big deal as long as you do not link the file/folder from other sites and visitors cannot discover it.
The real problem is that the same-named file/folder with different contents couldn't be added for different sites.
Article ID: 160
Category: WP Empire Builder