You don't have to make a backup of your GDFS, but you should do it before you start flashing or customizing your phone. If you do sth wrong it might save your phone. Your GDFS could be damaged and without a backup you might not be able to revive it.
The size will be rather small (around 60-100KB), because SE Tool lite doesn't make full GDFS backups. But it's enough to bring your phone back to life if the GDFS gets damaged.