[slijin]

Yes, those are the PWM cables. Do note that brown-red-orange is not the only color coding scheme for PWM cables (white-red-black, yellow-red-black, and yellow-red-orange are also accepted standards). Keep in mind that the USER button is the calibration button, and for your purposes (or at least your current ones) you should not be playing with this button. Messinig up the calibration will have serious effects on motor control and hamper troubleshooting.

Furthermore, that line of code does not initialize the Jaguars, but rather creates a RobotDrive object that will allow you to do so. See this edited sample code from the Getting Started Guide to Java:

public class RobotTemplate extends SimpleRobot {
  RobotDrive drive = new RobotDrive(1, 2);
  Joystick leftStick = new Joystick(1);
  Joystick rightStick = new Joystick(2);

  public void operatorControl() {
     while (isOperatorControl() && isEnabled()) // loop during enabled teleop mode
    {
      drive.tankDrive(leftStick, rightStick); // drive with the joysticks
      Timer.delay(0.005);
    }
  }
}

Emphasis mine. Of course, your code may be different, but keep in mind that simply creating drive does not generate a Jaguar signal, because you haven't created a signal source. The highlighted code above does that.