There is no way to easily configure gnome-shell notifications as of yet. You can disable them or configure them to time out.
dconf-editor allows you to configure some settings
sudo apt-get install dconf-editor
You can also modify
notify-send so the messages are transient.
# Move the current script to a backup location
sudo mv /usr/bin/notify-send /usr/bin/notify-send.bak
Now, use gedit for a new wrapper script
gksu gedit /usr/bin/notify-send
copy-paste this into that file
/usr/bin/notify-send --hint int:transient:1 "$@"
Save the script , exit gedit, and make it executable
sudo chmod a+x /usr/bin/notify-send
See also this forums post for addition suggestions.