Are you self hosting a dedicated server, or using a host service?
For self hosted dedicated servers, Xyth beat me to the punch
For hosting services (uHost, Blue Fang, etc...) when you log into the server's control panel, and you go to the file manager, this should drop you in the server's version of the [install directory]\SteamLibrary\steamapps\common\7 Days To Die folder.
From here you just upload the mod(s) folders/files into the Mods/Data/etc.. folders like normal.