If you set the jumpers on the drives so one drive is master, the other slave, it doesn't matter which plugs on the cable they're on. If you set the jumpers on the drives to "Cable Select", then the one with the black plug gets to be master, and the one with the grey plug gets to be slave. The cables are made with the black plug in the middle because UDMA/33 (and higher) drives don't want to be a long way from the controller; while it ought to work, you may find UDMA/100 and perhaps even UDMA/66 unreliable right at the end of the cable. The expectation was, you fit your UDMA/xx hard drive near the controller, and your DMA or PIO CD drive at the end where it's less affected by cable length.
Mark0999: Mixing devices of different speeds on one cable is supported fine by most chipsets. Don't let anyone tell you that hooking a UDMA/33 CD on the same cable as a UDMA/100 hard drive makes the hard drive run at UDMA/33. It's just not true. Of course the CD drive will take three times as long to transfer the same amount of data, and the aggregate effect will be that the hard drive appears to go slower than if you had an (otherwise similar) UDMA/100 CD drive, but that's not what's actually happening.
If you don't believe me, put a UDMA/66 hard drive on the same cable as an old Iomega ZIP 100 IDE (only does PIO mode 0, that's about 3MB/s); the hard drive will still zip along nicely until you try and access the ZIP drive at the same time, when everything will appear to go dead slow.