I don't think matching colors with the manual really matters (I think they're mainly colored on the board to designate what it what). The d/l link for your board's manual seems down now so I can't check it but here it is basically. Just take a look at it again and I'm sure you'll get it.
You'll see in the manual where the front panel connectors go and which pins are for what, whether it be LED or power, etc. They may also be marked next to the pins on the board as well. Different connectors use a different # of pins. For example, you'll see the HDD LED connector and there'll be 2 pins needed for it. You simply take that lead from the case and plug it onto those 2 pins on the board. Do the same for all the rest. It can be a bit tricky if they're close and you have bigger hands. Just match up the correct + and - and you should be fine.
Hope that's what you were looking for and it helps a bit.
Edit: From looking at a picture of the board, it looks like the connectors are the colored ones next to the SATA connectors. Just plug in each case lead into the corresponding pins on the board.