One thing to worry about is that when you plug the Wixel in to USB, its 3V3 line line will go up to 3.3 V. If your AVR’s batteries have discharged some, then the AVR could be running at a significantly lower voltage than the Wixel. There is a risk that the Wixel would partially power the AVR through the Wixel’s TX line. To minimize the risk of that, you might want to put a 200-1000 Ohm resistor between the Wixel’s TX line and the Arduino’s RX line, and another one between the Wixel’s RX line and the Arduino’s TX line just to be safe.
If you are using a 5V USB-to-serial adapter to program the ATmega328, then you should take appropriate precautions to avoid powering the AVR at 5V through its RX line.
Other than that, I think your setup will probably work.