Chances are, you were running in AHCI mode and the setup defaults switched your SATA controller to IDE mode. You may or may not have lost the data on those hard drives, sorry to say. There are ways of recovering it if you can move the drives to another operational computer, though. Try setting it back first, though.
OK, so when you boot into your BIOS, you need to go into the different menus until you see an option called "SATA OPERATION". Switch this from IDE to AHCI. Save and exit. And pray.