1) Simple method

- Connect to ARKREmote using ARKServerLauncher
- Go to the Mods tab in ARKServerLauncher
- Select mods in the mods list  and click on "Add" next to each mod you want to install
- On the left side you should see the  selected mods. For each mod you selected, click on the mod then on the Install/Update button as well as the Activate button on the right.
- Finally click on the Write to server button on the bottom right to update your GameUserSettings.ini file with the mods to load and restart server.

2) Manual method (deprecated, do not use anymore for now due to bugs with -automanagedmods argument )

To install mods on your ARK server you must first get their ID. This is the "code" of the mod that you find on the steam workshop. When you are on a mod page you will find the code in page url, for example:
https://steamcommunity.com/sharedfiles/filedetails/?id=722649005
Here the id of the mod is 722649005

Once you know the different mods ID's  to install, edit the Saved\Config\WindowsServer\GameUserSettings.ini file on your server from the control panel> config files

In the [ServerSettings] section Add a new line ActiveMods= followed by the mods ID's to install (separated by commas).

For example:
ActiveMods=722649005,721588929

Now edit the Game.ini file on your server from the control panel> config files

In the [ModInstaller] part (create it if missing) list the mods as shown below:

[ModInstaller]
ModIDS=758608778
ModIDS=566887000
ModIDS=558651608
ModIDS=854186603

Replace the mods numeric ID's by theo nes you want to be installed (one mod per line).

Save and restart the server.