I am currently using the ADC port on the px4 to arm/disarm the system with a button that will live on our rover. I wrote a simple script that monitors the voltage of the "sonar sensor" that the button is, and disarms the system if the button is pressed. I would like to have this code running continuously either when mission planner starts up, or when connection between the px4 and the GCS is established. It is not ideal to have to go in and select/run the script manually. 

Thanks, Seth

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Michael Oborne gave me the solution in this discussion on Ardupilot's forums 

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