With Publisher standard, you can only reload files that are in either your root folder or one of your mounts. With Publisher Enterprise, you get added "Source Document Folders" which split up this functionality. You can reload other files with Publisher standard using command line reloads and Windows Task Scheduler (to do a command line reload, you need QV Desktop installed on the server).
Regarding hiding files from end users, just make sure they do not have read NTFS permissions on the file. And, of course, make sure that your Publisher account has full permissions.