Command line options and config options are completely equalivalent meaning that you can just transfer them to a config file.
Simple example to translate any arangodb command line option into a config file:
Command line:
--server.endpoint tcp://127.0.0.1:8529
Config file:
[server]
endpoint = tcp://127.0.0.1:8529
So server is referencing to a config group here and endpoint is an option.
There is one exception: The database directory can be specified on the command line without explicitly using --database.directory.
Full example of the startup of the first agent:
[server]
endpoint = tcp://0.0.0.0:5001
authentication = false
[agency]
id = 0
size = 3
supervision = true
[database]
directory=agency1 # better use an absolute path here of course ;)