To add mods to the server, you must first subscribe to the content on steam workshop. Once the files have finished installing to your computer, you must find the installed folder (labeled by a series of numbers that matches the id of the mod in the steam workshop link).
The mod folder and .mod file will be located within the following directory of your client installation: /SteamApps/common/ARK Survival Evolved/ShooterGame/Content/Mods/
Now, you must stop the server and navigate to the //arkse/ShooterGame/Content/Mods directory of your server's FTP. This Mods folder does not exist by default, and must be created. Simply move the installed mod folder and .mod file from your computer onto the server's FTP.
Once the files have finished transferring, navigate to my.gameservers.com > Config and access your command line. Once here, you will want to add the following:
GameModIds=?
Once done, press submit and your server will be restarted.
Please note, mods are stackable, and can be seperated by a comma. An example of the command line is as follows:
TheIsland?GameModIds=123456,9789456,123455?Port=21000?