There are two types of mailboxes, user mailboxes and the m9999999 mailboxes. When you just add a mailbox, you get a m999999 mailbox. Whenever you create a user in the web panel, that user gets a mailbox with the same username. The difference is where the mail storage is located. A user will have access to his Maildir directory when he logs in to FTP, and can setup his own procmail filters, etc. However, a m999999 mailbox is stored on another server and you wouldn't be able to access the Maildir for it nor setup procmail fitlers for it (other than what you can do with web panel or mailboxes.domain).