Hi,
About your code.
master.mav.manual_control_send(
master.target_system,
0,#x
0,#y
100,#z
100,#r
0)
This is because of some legacy workaround, you need to use your z between -1000 and 1000.
This should not be a problem, you can connect the pixhawk in your computer, start mavproxy (mavproxy.py --master=/dev/ttyACM0 --out=udpbcast:0.0.0.0:14550 --console
) and after that run a simple script to arm the vehicle, the vehicle will continue armed after the script finish, you can even restart mavproxy and the vehicle will show as armed
Can you share your project/code to see what is going wrong ?