You should check the manual for your MOBO as to why they are color coded. SATA connectors are sometimes color coded to help you determine which chip (controller) they are using (if you have more than one SATA controller on the board). This can affect the speed at which drive will perform (1.5 Gbs, 3 Gbs) depending on the chip speed. The color can sometimes be use to determine if they support a bootable OS (usually RED means bootable, BLACK means not). And finally, even though you don't need a master/slave setup like IDE drives, you still have different channels, so those colors could help determine which channel each uses. If you don't have the manual, the board should be labeled next to each connector (SATA1, SATA2, etc.).

Otis