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Hi Timmy,
There isn't much to it really. All you have to do is use OS X Disk Utility to create an encrypted partition on your backup drive. Obviously you must choose a strong, memorable password using something like DiceWare or a random password generator tool like 1Password. I favour the latter personally. Whatever you do, it is very important that you eliminate any risk of forgetting that password otherwise the backup is useless.
After that, once the partition is mounted in OS X it just looks like another drive to SuperDuper and everything works just the way it normally does.
OS X gives you the option to remember the password for the drive in the OS X keychain so you aren't continually prompted for it each time you connect it to the computer you are backing up. Of course not having to type it frequently enhances your chance of forgetting the password unless you use something like 1PW.
Hope that helps.
K
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