essentially, the SATA ports are numbered in the order that your computer is going to want to access the information being sent trough them: Your system drive should go into port_0 or 1, depending on how your motherboard numbers everything. They should also primarily go into the first SATA port that is available on the on-board SATA ports; in your board's case, this will be the collection of brown-colored ports. The collection of black ports in the middle (four of them) are basically just slower data transfer rates: I would use one of those for your eSATA port for your front I/O unless you regularly use it, in which case I would recommend using that in one of the two brown ports. The other two gray ports are primarily there for the system to use for SSD caching, so unless you are doing that then those ports can be left alone.
So to summarize, your top two priorities for your SATA devices should go into the brown ports and the system drive should be in the first port (usually the top one). Everything else goes after that into the brown ports in order of importance.