Is your intended scheme going to be:
Computer -> Arduino -> Xbee (or other wireless device)-> Xbee -> Arduino -> Ardupilot?
For the Computer to Arduino part, see http://playground.arduino.cc/Main/InterfacingWithSoftware
. Covers pretty much every programming language you can think of.
For the Arduino to Xbee to Xbee to Arduino part, see http://www.billporter.info/2011/05/30/easytransfer-arduino-library/
. This library really simplifies communicating between Arduinos over serial, and since Xbees have a serial interface it kinda makes it a done deal. There are a lot of non-Xbee devices that have serial interfaces so an Xbee specifically is not required, but I'll leave it to your discretion as to what might work better. I do know that Xbees are frequently used with RC planes for telemetry so they're kinda tried and true there.
For the Arduino to Ardupilot part, see http://arduino.cc/en/Reference/Servo
. This would let you send commands to the Ardupilot using the same method that an RC receiver would.