In which I post a reference, mostly for myself, on how to update my chosen media server...
I'm not going to cover how to install Plex on FreeNAS as it is very easy using the plugins system explained in the docs.[1]
Upgrading, however, is a different issue. While the plugin does get updates that will preserve your data they are often quite behind the release schedule of the Plex team. Also I have had issues with some of my Plex plugins (like Trakt.tv) after using this upgrade method. In the past I have tried a hodgepodge of different methods to acheive it but now the most reliable method is using the PMS Updater script.[2]