I have everything plugged in besides the case fans, i have the MSI gaming 5 motherboard and the plugs marked case fans are 4 prong not 3 prong, how do i get this to work? literally everything else is running fine but the case fans
They will definitely fit. Note how there are 2 little ridges on the plug from the fan. Now look on the board and see how there is a tab sticking up. The tab goes between the ridges. You will have one pin left unconnected.
I am going to assume it is the NZXT Phantom. I can't find many close up images of the header wires. Do you have a choice of AC97 and HD? If so use the HD audio plug. The AC97 one is not for your board.