Suppose the application you want to start is called myapp.
Become root and create a file under /etc/init/myapp.conf
start on stopped rc RUNLEVEL=
./myapp -i /home/me/myapp/system.ini
Run "initctl start myapp" to start the app.
Run "initctl status myapp" to see the status.
Run "initctl stop myapp" to stop the app
Keep in mind that myapp should not daemonize itself. Upstart will do the daemonize part.