ich10r sata vs silicon image

I am putting together a computer, have an the p5q pro mobo, an antec sonata 3 case and a wd6400aaks harddrive. The sonata case has an external sata port cable.
The mobo has (6) ich10r sata connectors, red and (2) silicon image sata connectors, orange and white.

I'm only going to be using the single harddrive, what's the difference between the two sata connectors, and more importantly should I be connecting both harddrive and external sata port cable into the ich10r connectors or the silicon image ones?

thanks

that's what I've done, works fine.

thanks