Just put all the files on a folder of your website, then go on it with your web browser and follow the instructions !
The S-Update update server is to use with any S-Update client library, it's where the files will be stocked ! Just put your files in the files folder as they need to be download. Every files are checked. All the modified or deleted files are redownloaded. If you activate the included FileDeleter app in the client, all the unknown files will be deleted. To prevent a file or a folder to be deleted, just put its name into the S-Update-Server/Ignore.list file on the server.
Nothing ! It's totally automatic