What about the usb's?
Additionally,
What does normal operation look like on the red LED's?
The stock h100i has a 3 pin and Sata attached to it. After I plug the 3 pin into the board do I plug the Sata into the psu?
For USB, you can use either port but not both. There's just two to allow easier access with different mounting arrangements.
I'll put together a more formal document here soon, but the LEDs are grouped into four main categories. Beside each PCIe power input there's an LED which indicates whether there is voltage present on those plugs. On the right hand side of the board (away from USB) there is another LED by the 7V (actually 6.8V) power supply and test point that indicates that voltage rail is working. On the side of the board with the USB, there is one more LED by the 3.3V power supply and test point that indicates that the 3.3V rail is powered up.
Lastly, there is a row of 8 LEDs that are general indicators. Right now the top four light up when the board is on and running, and the bottom four will light up when the low voltage power supplies have been requested to be turned on. We'll probably fold more debugging information into those going forward, once we finalize all the information that we want to display.