Don't use your primary internal hard drive, i.e. don't partition it and put a backup on the partition. Disaster recipe for certain.
Your solution is either an online backup, like Mozy.com or Carbonite.com, get a time capsule, or get a hard drive. Hint: get a drive with firewire 800, it makes a difference. If you're lucky enough to have a Thunderbolt port, get a Thunderbolt drive, it is the ultimate.