We need more info to answer completely. The fact that your mobo's headers have 4 pins does NOT tell us what they are doing. They could use either Voltage Control Mode or PWM Mode for control. The only way to tell is by deciphering the info in the mobo manual.
The newer 4-pin fan system has a couple of backwards compatibility features in it. For your situation, it is this: IF the mobo header is using PWM Mode to control its fans, a 3-pin fan will always operate at full speed. This gives you full cooling, just no control. If they are using the Voltage Control Mode (aka DC Mode), they will power AND control your 3-pin fans.
Post back here what maker and exactly which model mobo you have, and we can help figure out what its fan headers can do.