The PWM channels use a pulsed 12V signal which is also a big difference to normal PWM fans for example. As you already mentioned they use the PWM signal for speed control but this signal is very different from the PWM signal which the aquaero provides. The PWM signal from the aquaero is designed to power things like LEDs for example or other stuff with a lower power consumption.

The RGB output can be used with our RGB-LED. You can use it in many different ways. For alarms or to show the water temperature by fading from blue to red etc.