PAD is easy — it's connected to the pad under the chip. AVSS & DVSS are connected in multiple places, hence the ambiguous numbering. More information on which pins they are is available from the datasheet.
In order to map the Arduino pins (like pin 13) to the pins on the Atmel128RFA1, you have a couple of options. One is to look at the headers the pins go out to. Each pin on the header is labeled with the Arduino pin number right next to it. Then trace back to the chip. Alternately, you can take a look at arduino/cores/zigduino/pins_arduino.c (-0021 based version) or hardware/arduino/variants/zigduino_r1/pins_arduino.h (1.0 based version), which have a complete map from the Atmega128RFA1 ports to the Arduino pins.