Well, Giga-Byte tech probably has some worth to it since they manuf' the boards they're talking about, instead of just being some dumb@ss WorstBuy techies.
...sorry...
Anyway, the performance is negligable at best, but if you can, like willsko87 said, connect one drive to one cable, and put the other drive on the other cable. If that doesn't fit your situation, then you have to make a decision.
1. If you have a strong computer, it doesn't matter which connector on the cable you put the drives on.
2. If you have a slow computer, and are a DVD fanatic, put the DVD drive on the end connector. Otherwise, put the HDD on the end connector.
3. Either way, your HDD needs to be master and your DVD a slave.
If you put them on their own seperate cables, you can probably set them both as master. This depends on how your mobo operates its IDE controller. Read the doco to find out.