I've had success with creating soft links in the data directory to places I want to access (but for my personal data only, haven't tried sharing them). Of course, the permissions still have to be set accordingly for OwnCloud to be able to access the files, but I think you won't get around that bit with any method.
For me, owncloud recognized the files all by itself (although it took some time). Currently I simply have two links to my Music and Photo collection, and both have been scanned (although the Music application doesn't seem to recognize all files, but I don't think that's related to the file access itself, since all the files are visible in the Files section). Even upload works if the directories are writable to www-data user.
With that approach, you can use every method of data access which is mountable (i.e. you can use ftp, ssh, smb and many more).
Edit: This method obviously only works for Linux servers - Windows users, sorry