>I'm working on a box right now, adding a secondary hard drive. The way it was designed, the IDE cable to the primary drive is short with only one connector for a drive. There is another IDE cable running from the mother board to the CD drive that does have the second connector, and is positioned in the perfect place for the secondary drive. Will that work or do both hard drives need to be on the same cable?

You can have a drive on each cable (the cables are connected to different controllers).

when you have 2 drives (whether HDD or CD or ??) on a cable, you need to look at the jumpers on the drives and make sure they are not both set as MASTER, or both set as SLAVE. One should be MASTER and 1 should be SLAVE. There is also a CS (cable select) setting, but that takes a cable with a twisted section in it which is usually not on newer machines.