Because the serial port is used by the XBees, the use of Serial.print() for debugging is kind of out the window, since the XBees in transparent mode will just send everything. I suppose it doesn't matter if the receiving end were to print extra stuff, that would be transmitted to the sending end, where it could just be thrown away. But whatever the transmitting end prints will be relayed to the receiver (and vice versa) and so I think it has to stick to just the data to be sent.
Guess I'm not sure what the best approach is, I hardly ever use transparent mode. But there should be folks around who maybe can make some suggestions. (I'd like to know, too!)
I think I said earlier, some other pins could be configured with SoftwareSerial, then something like an FTDI cable would be needed to connect back to a PC. Using an LCD is another idea.
Unless you happen to be using an Arduino Mega, which has four serial ports.
it is fun stuff, isn't it! XD