How can I share multiple drives?
Let's assume the server's home directory is set to C:\ftproot and you want to make your picture collection in D:\mypictures available as /pictures. Add D:\mypictures to the list of shared folders and select its entry. Next add /pictures in the alias column. Now the server will display the virtual directory pictures right in the root directory and its contents will be those of D:\mypictures. 

출처 : https://wiki.filezilla-project.org/FAQ#FileZilla_Server_FAQ