Is there a file I have to add the name of my cs file to?
You create the cs file in the Add-Ons directory (by writing one from scratch or copying an existing one, changing the datablock(blah) names and values of some things) and then enable it in the Add-Ons menu when starting a server. You do not need to add it to a file like game.cs/weapons.cs/etc anymore.
The ADD_ON_LIST.cs file in your Add-Ons directory shows what add-ons you have enabled, not what appears in the menu. (Any cs file in your Add-Ons folder will show up, including subfolders)