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I have an 80 gb intel x-25m in my 13 inch MBP but I also took out the superdrive and installed a 500gb live in an enclosure in the optical bay.

Yep, it is off when it isn't and use. It does affect battery a little bit but I have found it be negligible.

How does that affect heat and battery life? Does the second disk switch off when not in use?