Hi @johng,
The Navigator is a flight controller board, and does not have direct joystick inputs. I suppose if you use a serial to USB converter you could write some code to run on BlueOS that reads your joystick values and sends corresponding MAVLink messages to ArduSub, but that seems unnecessarily difficult if the primary aim is just to control a couple of thrusters, and presumably without a computer interface if you’re trying to connect the joystick straight to the flight controller.
Have you considered using a Thruster Commander? It should allow you to control two thrusters using a couple of potentiometers, with minimal fuss, or more thrusters with more commanders.
If using your specified joystick is important then I’d probably go with @john6’s suggestion of using a microcontroller to convert the joystick values into ESC control signals.