Interoperability XBee and ZigBee

Hi All.
I use severeal Arduino+Xbee s2 Module my project. So there is a API coordinator, API router and API end device, so the things works perfectly. I use xbee only for sending and receiving strings, no profile, no XBEE pins, nothing, only send Xbee's frame with string payload over the network.
Now I want to develop board that integrate the hardware of the coordinator, so I start to think to use a microcontroller like ATmega128RF that include IEEE 802.15.4.
How I can integrate the functionalities that I use on my XBee Coordinator in the ATmega128Rf? It is possible?
So,If I change the coordinator and leave all of the other node with ARDUINO+XBEE is possible to comunicate?
Thanks
Alessandro