3 pin fans control with voltage while 4 pin control with a duty cycle.
Now you have to watch out with splitting 3 pin fans as it places more load on the board.
This limit applies to 4 pin fans as well, but they take 12 volts all the time and the duty cycle tells the fan's motor how fast to go.
The adapter listed by the above poster is good because it prevents load on the board by making the power supply carry the load. Just ensure you only use 4 pin fans with that kind of adapter as 3 pin fans with it will run full speed all the time.
pwm fans(4-pin) will run on voltage control(3-pin) based fan controllers the extra pin just hangs off. It may not control quiet as well, but should work.
If you have multiple PWM headers, the adapter(a few of them) listed above may be a good way. Just remember you will have lots of wire to hide and only 1 of fans per adapter will report speed to the board.