OK, once you unzip the folder you will have your 7DaystoDie_Server folder, you can copy/paste and merge that with the folder of the same name on the server.
You can copy and paste the Mods folder as well.
For the data Folder, copy and paste the Config and UMA textures folders over and merge them.
However, with the Prefabs folder, you need to copy and paste the files inside the folder to the Prefab folder on the server. So go into the downloaded folder for DF, go into Data, Prefabs, press control +A to highlight all the files, then right click copy. Then Paste them into the Prefab folder on the server.
Also make sure you setup your serverconfig.xml before starting the server, game name, server name, server description and all the other settings.
One more thing, if you're server is running Linux, it's a more complicated setup and out of the scope of my knowledge. I setup a windows virtual machine just for my mod servers.