This is not really a problem. You should be able to select which of the HDDs to boot first in the BIOS settings. If you mess thigns up, no data should be lost anyway, and you'd be fine as long as you reverted to your previous setup.

Alternatively you could just reinstall Win7 on the 500 GB HDD without formatting it. The new Win7 installation will rename the old windows installation windows.old, and not delete any files. I've done this a few times myself. Works wonders.