First ... I appreciate taking the time to respond.
It would be commands. I want to fly the aircraft using waypoints, a subset of which will send a trigger to the companion board to take a measurement, and log the measurement with time and the GPS coordinate (including altitude). I might want to trigger a photo of each event as well.
I will read up on mavlink too. What is the mapping software used to graph the flight plan? Is it Mission Planner? Can those data be used to also display the flight in different presentations, e.g., from various perspectives? Could it also be annotated with the specific waypoint data such as time and GPS? Is there a resource of other software used for graphical presentation or/and data analysis ? (I know this goes beyond my initial question, but what the heck.)