I have a method that works for me, but may not apply to the way you want to organize things. I have the Media Library option off and am using Network Shares by connecting to Samba on a Raspberry Pi. Under the home directory for the logon I have 2 sub-directories: .HDD1 and .HDD2 (they start with a period so they are hidden from the WD scanning). My 2 hard drives are mounted to these sub-directories. In the home directory I have several playlists, one for each genere: Adventure.pls, Drama.pls, etc. Also I have a playlist named 1BigList.pls. this one has all movies in alpha order. I named it this so it sorted in front of the other playlists. Within the playlists, references can be to either hard drive. I don’t bother with any sort of organization when deciding on which drive to place a new movie. I do automate the process of generating the playlists, because that could be quite tedious to maintain.
In summary: The WD box sees only a single Network Share, so it looks like a single “drive”, but multiple hard drives are mounted under that directory.
