Just to add.
When you clone, you create an exact copy of the HD that you clone from. In my case, I clone to alternating external HDs that are the same size as my internal on a weekly basis over FW800. It's takes a few hours but then I have a complete image of my internal HD that I can boot from.
This way in your mind you know that only the clone files exist on the external HD. If you choose to store other files, you may end up accidentally erasing them when you clone. Additionally, I found that before I run CCC, I erase the target HD and run a quick Disk Repair on it before cloning so it is a fresh drive. Of course I couldn't do that if I was maintaining other files on the HD.