It should be a simple matching of headers to cables. The cables should have info printed on them to tell you which pins they need to be connected to. If you have the polarity reversed it might not work. If the cables are shifted by 1 pin in either direction they won't work.
Takes some pics and that might help decipher what the issue is. Also being a bit more specific with the exact model numbers of the case / mobo will aid in helping you figure this out.