Robot_upstart allows you to quickly and easily generate background jobs to run roslaunch invocations on system startup, but you can also use roslaunch without robot_upstart. You need to modify fcu_url and gcs_url in /opt/ros/kinetic/share/mavros/launch/apm.launch and run roslaunch mavros apm.launch. Roslaunch will automatically start a roscore if there isn’t already one running and you’ll get your Navio connected to GCS.
To run this on boot you can create a simple systemd service. Create mavros.service file in /lib/systemd/system with the following contents: