how does the motherboard manual explain the different specs for each?
SATA III 6Gb\s should be the fastest available.
i doubt you would really notice any difference in OS loading speeds depending on the port.
some may be designed for using a RAID setup with Intel Rapid Storage which could denote their different color.
some may be disabled when using other motherboard features which could also be noted by color.
To my knowledge there is no color standardization for sata port speeds. More often than not there are multiple controller interfaces on a given motherboard and the colors differentiate between them. You will need to read up on your motherboard interfaces to figure out which is the best for your application. Typically the fastest your drive can support is the best for the application. Often you will also find a raid (Redunduant Array of Inexpensive Drive) controller on one of them. Depending on how you set it up it can enhance speed in a multiple drive setup, but if only using one drive it will do nothing for you. Depending on your level of expertise I often will avoid setting up a boot on a raid array. They can be finicky, especially when updating bios, and in the modern era of SSDs the bandwidth performance gain can often be mitigated by the latency they create. Also most consumer RAID can either mirror or stripe, but often not both at the same time.
You'd have to consult your motherboard manual to see which ports use which SATA standard, as the colors are not standard. It also depends on what storage media you're using. For example, if you have a hard drive and a SATA 3 Gbps and a SATA 6 Gbps port, performance-wise they're practically the same. If you have an SSD, then you should plug it into the fastest port.
Last time I saw a mobo with color coded SATA ports it was some ... 15 years ago. If OP board is that old, it might actually matter where he connects his Windows drive. But without knowing what that boards is, pretty much anyone's guess ...