Developing my own drone

Hello,
i want to contribute in polish competition about building drones. I will build a simple drone, quadrocopter with attached sonar at the bottom of body which will land on water and collect data from underwater ground. But my question and problem is about developing this: I would want to use mission planner to plan my mission in real life, but after every landing on waypoint there is a need to start working sonar. How should i manage it? Should i customize MissionPlanner, make customs in ArduPilot autopilot code or make a python script that will start “recording” at every waypoint? Also i want to show live data on screen(PC or dedicated console), so how should i take the problem?