To to update manually into my Apple TV:
1. Upload the boxee file into ATV with sftp
2. Get the latest script to update:
wget http://atv-xbmc-launcher.googlecode.com/svn/tags/boxee-info/scripts/alpha-0.9.11.5591_update.sh
3. Run this:
sh alpha-0.9.11.5591_update.sh boxee-0.9.11.5591.dmg
4. Reboot:
sudo reboot
Enjoy!