The ATxmega128B1 can be programmed through the USB interface. This can be accomplished using the USB boot loader that is preprogrammed in the device.
The boot loader is evoked by shorting pin 6 on J1 to GND before applying power to the board. A 100mil jumper can be used. Programming is performed through the FLIP application mentioned in Related items
Refer to A functional overview of the Atmel XMEGA-B1 Xplained kit for the location of J1 header.
Note
If any external programming tool is used on the ATxmega128B1, the boot loader might be erased, and it will not be possible to program the device through the USB interface. In this case the boot loader has to be restored (available on the Atmel web site) with an external programming tool.