The default hardware configuration of the power supply block implies that:
The power supply sources are the battery or the USB plug (thus the dotted-lines on the J2 plug in the block diagram, figure AT32UC3L-EK Power Supply Logical View and Figure 1
The power-off signal from the AT32UC3L064 is not connected to the on-board power supply block (thus the dotted arrow in the block diagram)
To enable the power supply through the J2 connector, mount the R5 resistor (solder patch) and remove the R6 resistor.
To activate the Power-Off signal, remove the R17 resistor and mount the R26 resistor (solder patch).
To locate the resistors mentioned here above, use the assembly top/bottom views provided within the AT32UC3L-EK schematics package.