Thinking more about the project, it would be awesome if I could use a micro controller with 2 UART ports to talk to both and programme them with the push of a button.

I am going to try to write a program that will pair two xbees without having to enter all the configs each time.  I should be able to use the AT commands to read the serial numbers and set the other configs appropriately.   I should be able to make it work easily if I use two Xbee explorers. Otherwise, I will have to make it read the first xbee, program the second and then program the first again with user prompts in between to change out the xbees.  I think the first option is the best though.