Okay, look at your motherboard from this orientation so we're both looking at the same thing in the same way.
On the bottom of the motherboard, just above and to the right of the notation "MADE IN CHINA", is a group of pins with the notation above that reads "PANEL 1". That's where your Power switch, Reset Switch and LED lines will plug into.
Look at the eight pins in the nine pin panel that form a box of two rows of four pins each. Those are the actual pins you'll be using. Ignore the one on the bottom row that's off by itself. Shuttle does, so we should as well.
Now, to the right and down of PANEL 1 is a little drawing on the motherboard of PANEL 1 with little lines and numbers and such. This little drawing shows you which pins are used for which lines. It looks kind of like this...
2 4 6 8
'MSG ' PWR '
'LED ' BTN '
'HDD ' RST '
'LED ' '
1 3 5 7
Lastly, as PANEL 1 has a little "+" right next to Pin #2, and we don't have a manual handy because Shuttle seems to have all the information available on the web except a copy of the bloody manual, we're going to take an educated guess that for each two-pin part of the box, when plugging in the individual plugs, make sure the black wire is the one on the right, and the colored ones will be on the left.
So, plug the Power button into the upper-right two pins, black wire on the right, Reset on the lower-right, HDD LED on the lower-left and the Power LED on the upper-left. (I'm guessing that's what "MSG LED" means. There are no "Power LED" pins anywhere that I could find.
This should take you only a couple of minutes, so post back if you have any difficulty. If you need a hi-res image of this motherboard, go to the below link.