If you are talking about the connecter being like the connecters from NMBs, you can jam the connector into the pins for a temp solution. Otherwise, if the connector is about the same as a 3 pin connecter, just missing the last pin, you may just need to sand off one edge and stick it bottom two pins.
Regular connecter:
___
_ . | <--- speed of fan
| . | <--- 12V line
_ . | <--- Ground line
----|
So for your case if the 2 pin connector looks somewhat like the bad drawing then you need to connect it to whereever the last 2 pins go (ie don't plug it in into the speed line). The best way would be to splice your wires and connect it that way.