Multiple Internal Disks
Booting Windows or Linux from the second (third, fourth, ...) internal hard disk through rEFIt currently does not work as expected.
According to Apple’s Boot Camp FAQ any internal disk works, so you may be able to boot from the second disk using the built-in boot menu. Hold down the Option key during startup to activate that boot menu.
It may be possible to properly support booting from the second disk in rEFIt, but the author currently lacks a suitable test system. If you can help investigate this and are willing to test patched rEFIt builds, please get in touch.