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I have two physical harddrives in my Mac. One is an SSD with the OS and apps. The other is a 1TB HDD for media. Can I setup time machine to backup both drives to time capsule?

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Yes, by default Time Machine will backup all internal HDD's whether they are SSD or not. Just make sure your time capsule is big enough.

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+1. Time Machine will also backup external drives plugged in to your Mac (except the Time Machine drive, naturally). – jaume Jun 16 '13 at 19:23

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