You will most likely want to customize your server's name, password, security settings, and so on with a server.cfg file. To change the Arma 3 directory and create and edit your server.cfg file.

cd ~/steamcmd/arma3
vim server.cfg

If you don't know how to use vim, use nano instead.

nano server.cfg

See server.cfg for documentation and examples.

The first time you run the server it will auto-create a profile file at ~/.local/share/Arma 3 - Other Profiles/server/server.Arma3Profile. Edit this file to fully customize difficulty settings. NB: the -profiles= parameter is broken on Linux - you must place your profiles in this directory.