It really depends on your motherboard - there is no standardization as to what colors mean for SATA ports on different motherboards. You will have to refer to the manual that came with your motherboard for clearer identification.
Commonly, SATA ports on a motherboard that has different colors can be categorized as such:
- Primary SATA controller ports
- RAID-capable SATA controller ports
- Secondary SATA controller ports
Usually, the color that has the most ports are the Primary SATA controller ports (usually black). The color that has even number of ports (usually 2) are RAID-capable (if your motherboard supports it, and I've seen yellow and red), and the secondary SATA controller ports are usually red in color.
Some manufacturers might even color ports just to help user ID what ports to use for an eSATA bracket.
Hope this helps. If you were to tell us your motherboard model, we could probably ID them for you.
EDIT : Found the port layout schematics for your M2A-VM.
You only have 4 SATA ports on your M2A-VM. 2 are marked black, 2 are marked red. There are no distinction in utility for all 4 ports, black SATA ports are ports 1 & 2, and red SATA ports are ports 3 & 4. Just go in serial starting from port 1. It does not affect anything at all.
Link to your motherboard manual here (PDF link).