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.