Actually, you can control your fans with 3-pin too. Its just not controlled by PWM technique. Your mobo will try to adjust the fan speed by raising/altering voltage. Just check your bios settings to see if you mobo can do that.
Another solution would be a Fan controller board. They are relatively cheap. You can easily get them and directly connect between psu and fans. You can find them either PWM or Voltage controlled versions. Just make sure if your fans also support PWM, all fans (basically all electric motors) can be controlled directly with Voltage.