Autopilot Designing

Hello, I have got a project of designing an autopilot for an amphibian UAV with  waypoint navigation facility. I have difficulty in working on C programming. So, I feel it is better to work in MATLAB programming. But, I do not know how to do programming for autopilot or in other words, from where should I start? Most probably I am going to use the Pixhawk Board. Please guide me.

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