All Add-Ons must have either a Server.cs or Client.cs to run whatever is in the Add-On's .zip. Some people only use the Server/Client.cs to execute their own .cs files, while others just put their scripts straight in the Server/Client.cs
If you put a separate .cs file for you scripts, you must put a exec for it in the Server/Client.cs
Add-On's are mainly Server.cs since they are, well, serverside. Add-On's like GUI's (Such as NiXiLL's LSG GUI) use Client.cs so they are executed on startup.