You don't need an OS on the second hdd; it can be used for storing data without an OS.
Backing up emails depends on your email client. If you use something Becky from click here it has its own folder where all data is saved and this can be on a seperated drive / partition. If OE, then you can open the address book and choose "export" from under the file menu.
Have a look here for info on backing up: click here