I'm just getting started on my first UAV plane and the plan is to have it be controlled from a James Bond-esque suitcase with a joystick and screen packed up inside. The picture below shows my (very) basic plan. If you notice anything major I should change please let me know.
On another note, I have almost zero experience in programming and am having a hell of a time getting the Arduinos to communicate with anything else. I plugged the joysticks into the USB Host Shield but I couldn't see that there was any form of dialogue going on from the Arduino software on my computer.
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Gobind, I'm working on a project sort of similar to what you're doing. You should look at this project:
http://www.rcgroups.com/forums/showthread.php?t=1231017
Using an Arduino to drive a transmitter. This would be a better way to go, as there will be much lower latency than trying to control the aircraft via radio-modem. Simply uses a joystick into an Arduino, which creates a PPM signal to output to a Tx. You can use the FrSky DIY Hack modules for $15-25. That, into an FrSky D4R-II Rx for $20, use the PPM-Sum signal into the APM 2.5, and you're good to go.