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 available from the website mentioned in Related items.
Refer to Figure 1 for the location of J1 header.