If you are referring to the fan having a 2-pin connector, and the board having a 3-pin connector, we need to know if you mean a 2-pin Molex. If so, you can either use an adapter to plug into the MB header or plug the fan directly into any Molex from the PSU. If you mean a connector that matches the MB header, but only has 2 pins, just plug it in using the guide and it will use just the two MB pins necessary.
When I said 'guide' I was actually referring to the 'key' on the connector. Sorry about the confusion. If you have a 2 wire fan cable with a MB header-type connector, it will fit the 3-pin MB header by just using 2 of the pins; the +12V and ground. The 3rd pin is for tach feedback, which you won't have with a 2 wire fan. So your fan will always run at 100%.
Thanks, I got it, but it actually was in my motherboard manual and not on the mobo itself (the ground vs 12v indicators) but its working now thanks. And these fans are cheap anyways its ok for it to run at 100%