Unless you have installed the Duet WiFi in an enclosed space with no ventilation, or right next to your heated bed, it is unlikely to need any active cooling with motor currents up to about 1.8A. You can read the CPU temperature on the web interface, but you need to calibrate it as described in the wiki. Even if the board was overheating, it is unlikely to slow down. I think it's more likely that the Duet is receiving an abnormally high rate of interrupts from one of it input sources, such as the WiFi module.
You should configure just fan 1 to be the thermostatic one (which it is by default anyway) and leave fan 0 as the print cooling fan. If you have 2 hot ends each with a hot end fan, either use fan 1 and 2 outputs to control them, or connect them both in parallel to fan 1 output.