Describe for us your setup, we need to know how your system is setup. You say you already have 2 hard drives and you want to add a third one. How are your 2 current hard drives configured right now? For example, 1 hard drive is primary master, the other is a secondary master; and the 1 hard drive has Win2000 on it, the other drive is just for storage, etc....
And you say have a PCI IDE card but when you attach the 3rd hard drive to it the drive isn't detected. This is usually a result of an incorrect jumper setting on the drive. Some drives require the "cable select" jumper setting. And are you sure you installed the right drivers for the card?