Create a custom commandline via the Commandline Manager, add the WorkShopModIDs of the mods you’d like the server to launch.
Make sure you check box boxes for: Enable Auto Mod Updater/Installer: in the Commandline!!

Gif Showing how to setup a custom commandline with mods

Go to your Configuration Files, Game.ini -> Configuration Editor.
Enable the Auto Mod Installer/Updater by checking the checkbox.
Click Add Mod and enter one of the Mod’s WorkShopModIDs into the box. (Repeat for number of mods needed)
Click Save, and check your Game.ini -> Text Editor to ensure it’s added them correctly.

Gif Showing how to setup the automated mod installer downloader

That should be it! Your mods will now stay up to date, or the server will update them the next time the server restarts. If it’s the first time you’ve added that mod, the server will download it next time the server starts up.

Happy Arking!