Hi jun,
Sorry for the late reply,
Yes, ATmega168 does not only control the wireless module but also can use as an Arduino.
Do you mean using RFBee to control the local led or the remote led?
If local, you can add several lines of code to RFBee.pde, for example:
…
#define LED_GREEN 5 //PD5 on RFBee
#define LED_RED 6 //PD6 on RFBee
…
void setup()
{
…
pinMode(LED_GREEN,OUTPUT);
pinMode(LED_RED,OUTPUT);
digitalWrite(LED_GREEN,HIGH);
digitalWrite(LED_RED,HIGH);
…
}
void loop()
{
…
}
If you want to control LED connected to the remote RFBee, then you need to do send the protocol data defined by yourself to the remote RFBee. And you need to add some code to the firmware on remote RFBee to parse the data, and then do corresponding control on the LED.
We are planning to add this function in firmware version v2.0, though v1.1 is about to release 
May this helpful to you, and please feel free to ask any question.
Regards,
-Icing