UsingGround Station to programatically control UAV?

So me and a team of college students recent purchased an X8+ octocopter.

We've done test flights using the remote control but now would like to do more refined controls... specifically we'd like to control the flight using a software program.

We were thinking of using C++ or C# to control the drone using our keyboard or arrows on a GUI we develop. We would find a way to use the source code from Mission planner to send altitude, loiter and positional signals to the drone.

 Is this possible? Is there a big hazard we should look out for doing this? If so, has it been done before or could someone point me in the right direction?

The X8+ has a site on 3drobotics: http://3drobotics.com/x8/ 

I attached the operation manual for the X8+ if you wanted to look into it: X8%2B-Operation-Manual-vC.pdf

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