what type of 2 pin connector is it ?
you can buy these if its same like this but just 2 pin.
http://www.sidewindercomputers.com/3pinheaderkit.html

if its a totally different connector you have to crimp (you can search youtube for videos on how to crimp fan) these on
http://www.sidewindercomputers.com/fepifor3he.html then put them into
http://www.sidewindercomputers.com/3pinheaderkit.html

if its just a 2 pin connector thats basically the 3pinheader without the speed sensor you can cut / sand of the indents and slot it into the mobo just find. refer to another fan to know exactly which is the correct point to connect to.

Red is always in the middle.