First of all you need to set up the second drive as a slave by changing the jumpers on the drive. This should enable it to be recognised - if not check in the BIOS to make sure that the secondary HDD is set to auto. Once you have done this you can back up your data to this slave drive and format the originalC drive.
I assume you have an original ME Setup disk to do this and you`re not relying on a recovery disk.
Boot Disks from click here