None of my case fans are two pin so I can't connect them to the motherboard. I just use the 3 pin connectors that are used for connecting things like the HDD. I mean there are two wires coming out of the fans but they join up with these larger 3 pin connectors. Maybe it's not the same for you.
edit - wait no, upon further inspection the pins are actually 4 on mine. Nevermind then...totally different.