You believe you misunderstood. I am also implementing my own control algorithms. In fact, my EB system could easily be used to control an airship. I read the PWM rail output of the EB (which is running ArduPilot), then apply my own control algorithms on the Arduino, then (re) send that output to the servo motors. It was much easier to do it this way than modify ArduPilot. I also use the mraa and upm libraries, on the Intel Edison chip that is in my glove. For an airship, I would recommend using the EB with a Raspberry Pi as the companion computer. I'm using an Arduino Due (which has a PWM library). Also, you way you "want to deploy your own control algorithms". You can't on the EB, it's already running ArduPilot which already implements control algorithms. You CAN send it commands via Python through ROS, but not PID control commands. So what you are suggesting is to write an entirely new autopilot on the EB, and not run ArduPilot at all. You would have to stop the APM service, then code yours from scratch, access the sensors directly, etc. A HUGE chunk of work. Instead, I would suggest that you leverage ArduPilot, and just modify it's output via hardware/Python.