Quick answer as I'm browsing via an intermittent internet connection at the moment.
Are you running this under windows, or a linux environment? For linux, we use the appdynamics service for the machine agent, and have that linked to /etc/rc3.d as a typical service.. I imagine you could do the same via a systemd service as well, though we haven't done so ourselves as of yet. Either way, if you have the service installed, it's pretty straightforward to set up. I'd recommend you start it after your network services though, as it will probably need DNS to function to find the controller, or the agent won't start.
For windows, I believe it's a service so you could set it to auto-start via the services application.