I and my research team are working on a novel drone design based on trirotor. The difference between this design and a trirotor is that it has an extra propeller to generate additional thrust, therefore we can not use the open-source autopilot ArduPilot anymore. I have prototyped a control algorithm on MATLAB/Simulink but I don't know how to implement this algorithm on the drone. I have encountered this on so many papers but I still don't know how they did it.
What type of hardware and coding should I need to prepare and learn in order to realize the algorithm? Should we continue to learn and modify the source code of open-source Autopilot like Ardupilot or it would be easier for us to start from scratch with a hardware?