OK, I’ll try to clarify things. There is one hardware serial port on the Arduino built into the EL Sequencer, and that single port is connected to both the XBee and the FTDI header. You can use either connection but not both at the same time. If you’re going to program the board with an FTDI, unplug the XBee while you’re doing it. Then when you want to use the XBee, unplug the FTDI, and plug in the XBee. Always use one or the other.
You can develop your code with the FTDI, and send it commands using the serial monitor and keyboard, or any software that can send data. Then when you’re sure the wired link works, disconnect the FTDI, and plug in your XBees. (You should configure your XBees ahead of time to automatically connect with each other.) This way, the only thing that has changed is wired –> wireless.
I hope this helps answer your question, please let us know if things are still unclear!
