Using the Arduino software with the Wixel shield for Arduino is not any different than using it normally, except that you will be programming on the COM port associated with a Wixel rather than one associated with your Arduino. In the Arduino IDE, select your Arduino board using
Tools->Board and select the the COM port that corresponds to the Wixel connected to your computer using
Tools->Serial Port. The upload button and the serial monitor will now work exactly like they do when your Arduino is directly connected to your computer via USB.