See: resource.AddSingleFile and G.AddCSLuaFile- includes example usages.
If you plan to primarily host a custom gamemode, you should check the gamemode's website or readme about specific settings to place in your server.cfg. Most server.cfg files are set up to handle Sandbox gamemode and its derivatives. This file is used for storing you server's identity, default settings, and information for user management and logging purposes. Server.cfg is the name of the configuration (.cfg) file that runs every time your server is started and every time you change maps.
See: Server Settings- includes an example server.cfg at the bottom of the page.
For additional help, see: General Server Setup Information.
For Linux, see: Linux Dedicated Server Setup.
For Windows, see: Windows Dedicated Server Setup.
Installing SCRDS, Garry's Mod, and default server configuration settings: