Cloning question

I have had my Mac Pro for about 6 years and it has been great.. The other day the system disk was giving me fits, potential bad blocks on the original WD 320 disk. At first I thought I was going to have to reinstall the OS, on my PC's I used a program called Acronis to clone system disks and it worked flawlessly. So I got to looking and found Carbon Copy Cloner, I have 4 disks in the Mac, in bay 3 and 4 is a striped RAID array for my photos. bay 2 is a 500GB disk I use for scratch files for Photoshop. Of course in bay 1 is the system disk. So I wiped out all the scratch files and cloned the system disk to the 500GB disk in bay 2. Once it was done, I moved the new system disk to bay 1 and put a new disk in the carrier a 1 TB disk and put it into bay 2. Boot the system, it was really slow to come up. For some reason, the system labeled the drive in bay 2 as /dev/drive0, which meant I could not format it. The system thought it was the system disk for some odd reason.. If I pull the drive out in bay 2, the system boots up and thinks the 500 GB disk is /dev/disk0s2. I need the disk in bay 2 to be my scratch disk again, but I can't do anything with it.. Ideas????