If your board is similar to my Asus P5B-E, the CHA1 and CHA2 will allow you to control the fan speed, while the PWR header will run at full speed all the time. So, if you want to reduce fan noise you could hook up one of the rear fans (presumably further from where you sit and less of a concern for noise) to the PWR header to run full speed all the time, while hooking up the other two fans to the CHA1 and CHA2 headers, allowing you to control the fan speed if you choose to.
As Lmeow stated, the 4 prong header is for fan speed control using pulse-width modulation. It is fine to hook up a 3 pin fan to it - you won't be able to use PWM to control the fan speed, but I would imagine you'd still be able to control it the old fashioned way, by reducing the output voltage from 12V to something lower for a slower fan speed.
I personally use Speedfan to control my fan speeds.