Hi @DuncanODL, welcome to the forum 
One of the example extensions includes PWM control, but that’s intended for if you don’t have a flight controller board connected.
From your initial post it seemed like this may have been your situation, but given you seem to be doing this as an extension of an ROV setup it completely changes which options are available, and how straightforward/involved they are.
What kind of control do you want over it (in terms of input and output, especially around gradations / speed levels)?
If you only want a few speeds you should be able to assign it as one of the incrementally controllable servo outputs ArduSub supports, and control it with joystick buttons and/or on-screen buttons in your control station software.
If you want smooth control over the speed then with Cockpit you could control it with a slider (although I’d recommend using a direct servo function over a lights function in this case, just to avoid confusion).