how to run a pixhawk without a USB cable?

Howdy, I currently have a PD program that will stabilize my system, but it's currently running on seesaw system and has a USB cable connect.

I want to remove the cable, but still run my program and collect information. If I create a daemon app with my code will I be able to connect a battery to the pixhawk then as soon as the system arms will my PD code start working automatically?

Currently I send the command to run a txt file that stops the commander and does some other options then I send a command to run my code using mission planner, how can I have my pixhawk just run my program automatically, without needing to send a command through USB.

Or could I use telemetry to send a command thought mission planner to run my program?

I'd prefer the first option, but the second one works too.

Thank you for the help!

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