Now that you've installed Ninja OS, you'd want somewhere to put your data. You need to make a second partition to store data. As for ninja os 0.6.3 clone and forge scripts automaticly make a second partition that fills the disk. This partition is empty, format it as you wish.
Start up Ninja OS
Click Applications Menu -> System -> Disks
Now find your disk on the right. Click on the empty space. Click on the little plus symbol underneath the diagram.
Now click on "type" for the following options-
no encryption - select "FAT"
LUKS encryption - select LUKS+EXT4. Note that neither ext4 nor luks will work in either Windows or OSX
Truecrypt Encryption - Leave as default,Follow this guide afterwards
http://www.truecrypt.org/docs/?s=creating-new-volume