For years I have used “.” in front of the libraries I wanted to show up first in the list. I.e. “.Movies” “.TV Shows”. Today however, the list order is the same as the server libraries order in settings under “Manage”, “Libraries”. I’m running the latest Plex Beta for server. Plex-for-Kodi is version 0.2.1.
Not sure what has changed the list order of the libraries.