I have this board and I agree with you on the manual. Did you notice they showed pics of another MB when they were talking about installing the cpu? Of course the manual isn't clear, it doesn't matter which way they are plugged in for the power because there are only two wires(a switch doesn't care which direction the current is flowing). Basically color doesn't matter. In the manual it gives a diagram of two rows of pins,
I will refer to them as row 1 and row 2, row 1 is on the left and row 2 is on the right.
just for example...
Row 1 Row 2
- -
- -
The upper first two pins of Row2 are the power, it shouldn't matter which way they are plugged in, if it doesn't work one way than obviously try the other. In the middle of Row 2 is a set of 4 pins, the bottom of the two are HDD Led lights. Again it shouldn't matter but if it does than switch it around. For the Power LED go to Row 1, the top set of pins. The bottom three pins are the ones you are most concerned with, the wires should be connected to pins 1 and 3
I hope this clears things up for you, if it doesn't shoot me a message back. Good Luck!