Ok I got my boards and I finished building them yesterday.
I followed the instructions on the pdf but I used my arduinos without the atmega chip with the pins jumpered.
RTS (pin 16) => 3.3V (pin 1)
DTR (pin 9) => GND (pin 10)
I can flash the xbee units but it fails because reset does not seem to be working. I have tried using both reset buttons(Xbee and Arduino) It seems that the unit does get partially programmed. The function set is changed but the node and PAN ID are still the same.
Thoughts? thanks for all the help so far.