Our team has a motor which we want to have somewhat precision control over. This motor is not a drive motor, however I was wondering if I would be able to define it as a drive motor and control it with the Y axis of Joystick 3. Would there be any problems from doing this?
You should open it as a regular motor (Acutators > Motor) and use the Set Output VI to control the speed. The Y axis of the joystick gives values between -1 and 1, which is exactly what the motor SetOutput VI accepts - so if you want you can connect it directly.