I just tried to do that myself but failed. The manual install worked. I followed the instructions on the setup info tab. After the update, the only way i could get it to run was by deleting a plexmediaserver symlink in the /etc/init.d/ directory and renaming a backup file that was in the same directory. Even then though it still didn't work through the web interface. I had to start it manually through an ssh session. I just had to uninstall and reinstall a few times to get it working on 0.9.11.13 again.
I too would like to know if there is a correct way to do this or if I am missing something.
Thanks,