I think you will need a copy of the Mobo manual. This will tell you the configuration of the pins and voltage. If posssible though there might be little markings on the Mobo itself to show you what goes where.
My power supply messed up so changed the case and I to had trouble getting it back connected, as i had not written down the configuration for the reset/on-off switch and hdd and power led's.
It was a case of trial and error till I got it right. The double connector pins may not align to just 1-2 3-4 and so forth, they may bridge between pins 1-3 2-4 if you get what I mean.