[pblankenbaker]

For your shooter, I would not use the RobotDrive class but recommend that your read values from your joysticks and then apply the current values to your shooter motors. Here's an example of a slight refactoring of some of your code:

public void operatorControl() { 
  while(isOperatorControl() && isEnabled()) {
    myDrive.arcadeDrive(driveStick);
    updateShooterPower();
    Timer.delay(0.01);
  }

  // Stop motors
  myDrive.stopMotor();
  M1.set(0);
  M2.set(0);
}

private void updateShooterPower() {
  // Read in joystick values from second game pad
  // (returns values in range of -1.0 to +1.0)
  double m1Power = driveStick2.getRawAxis(2);
  double m2Power = driveStick2.getRawAxis(4);

  // You might need/want to adjust power values here, the following example
  // treats values close to 0 as being zero

  if (Math.abs(m1Power) < 0.05) {
    m1Power = 0;
  }

  if (Math.abs(m2Power) < 0.05) {
    m2Power = 0;
  }

  // Apply power to shooter motors
  M1.set(m1Power);
  M2.set(m2Power);

  // If the joystick values or motor connections end up being the opposite of
  // what you expect, you may need to invert the power applied to one or
  // both of the motors.
  // Commented example of how to invert the power applied to both motors:
  //M1.set(-m1Power);
  //M2.set(-m2Power);

}

NOTE:

• You will need to experiment with the Joystick axis values (I showed 2 and 4 above, 1, 3 and 5 are also available).
• If you want to apply the same power to both shooter motors you will only need to read one joystick axis.
• You may need to negate (invert) the power applied to one or both of your motors in order to get them to spin in the proper direction.
• The Y-axis on gamepads tends to return -1.0 when pushed all the way up and +1.0 when pulled all the way down.