The J8+J44 expansion headers gather signals multiplexed with the JTAG signals on J8.1, J8.2, and J8.5. For this reason, JTAG debugging is not possible when an external component is connected to these pins of the WLESS header. See also Section Special Considerations for the RESET_N Pin and the JTAG Pins.
The J14 and J15 headers gather all GPIO signals of the AT32UC3L064. Obvious care should be taken when accessing pins that are being used by another component of the kit.