http://smyl.es/the-ultimate-nas-media-center-with-debian-based-openmediavault-and-plex-media-server/
This is the init script for Plex Media Server that should be located at /etc/init.d/plexmediaserver. This is something I had to track down when setting up Plex Media Server with OpenMediaVault, as the default installer for PlexMediaServer seems to have a problem with creating the init script, so I had to manually add it.
I've also created a script that will automatically install latest init.d file and do everything for you (move files, etc) https://github.com/tripflex/iPlex
wget https://raw.github.com/tripflex/plexmediaserver-init/master/plexmediaserver
mv plexmediaserver /etc/init.d/plexmediaserver
chmod +x /etc/init.d/plexmediaserver
Using this should be just the same as you normally do, but as example
/etc/init.d/plexmediaserver {start|stop|restart|status}
If you upgrade plex using the deb, the installer will rename the file to something like plexmediaserver.bkup, you will just need to remove the new /etc/init.d/plexmediaserver it created (should be blank), and move the backup back to it's original name.
Profit!