[Joe Ross]

Almost everything in WPILib and the documentation assumes that the sensor is plugged into the cRIO. This includes the PIDController class and PIDSubsystem, etc.

The CANJaguar class is what is used to do PID on the Jaguar. You set the appropriate mode (vbus, position, speed, or voltage) and configure all of the appropriate options. I recommend getting your desired mode working with BDC-COMM first and then copy those options to your robot code.

Other people have posted code using the CANJaguar class, I'd suggest doing some searching.