The PWM outputs are to provide a PWM signal to something else that you want to provide a PWM signal to. For example a motherboard CPU fan header, so that you can have the motherboard shut down the computer instead of the AE 5 shutting it down.

I believe that you can also set the AE 5's alarms to control the PWM output signal. Under alarm actions you can set it to turn on or turn off the "Tacho Signal," and other actions as well, depending on different parameters. The parameters are controlled by the alarm configurations tab, and that is where you can set the AE 5 to trigger various alarms, depending on reaching/exceeding/or not reaching certain parameters. You set the actions it takes for each type of alarm under the alarm actions tab. The options include turning the PWM signal "Tacho Signal" on and off.

The two 2 pin PWM output connectors are intended to provide power for LED or Cold lights. They do NOT provide an open collector type speed signal for a motherboard connection. For the Tacho Signal there is a three wire fan header connector marked "Tacho" for this purpose.

The two pin PWM outputs are controlled directly from the controller tab of AS2012 just as a fan would be.