Start up from your system installation disk by inserting the disk and starting holding down the "C" key. Go to the second screen pull down menu to Utilities > Disk Utility. See if both drives show up in the left hand column. Is so try repairing both. If just one drive shows up, thats the good drive. If both drives are the same make then put a system on it. Now remove the case. Disconnect one of the drives and try to boot. If the machine boots with the new system, the disconnected drive is the bad one. If it fails to boot, reconnect the drive and disconnect the other one and try to boot.