If you want to use an external hard drive (or USB stick) as your main storage on the Raspberry Pi, you need to jump through a couple hoops to properly mount it and make sure it loads up on boot. Adafruit made that process a bit simpler.
With just a couple of lines of code, Adafruit's script makes your external hard drive the new root hard drive and boots into that automatically. You'll still need an SD card, but otherwise pretty much everything you do will happen on the external drive automatically. Head over to Adafruit for the full guide.