I’m home now @travissolaman and I’ve reminded myself. The first thing you need to do is go into the Plex server addon settings (My Add-ons> Services> Plex (LinuxServer.io). When you go into the settings, you’ll see that you map where your movies, Tv Shows and photos are. The defaults are to /storage/videos etc. Change them to var/media/whatever. In my case I’ve set them all to var/media/TOSHIBA EXT/Media cause that’s what my HDD is called and all my Media is in a directory called Media (wow that’s original). I set at this level because I have music directories on TOSHIBA EXT/Media that I wanted to add to plex and there’s no setting for music in the addon .
Once you’ve done that perhaps a reboot would be in order. After that, go to the plex webpage and when you go to add a library you should see the folders from your external hard disc if you look in “data” directory which will be about half way down the list on the right hand side of the screen that comes up when you click on Browse for Media.
Hope this helps. my second paragraph is a little vague as I can’t recreate your scenario - a server with no libraries but I think it was the steps from the first paragraph that was stopping you.
Let me know how you get on please.