Step 1: Login to the Game Panel and press the 'stop' button on your service.
Step 2: Set automanagedmods in your Custom Commandline.
To do this, open the Commandline Manager and select the Custom Commandlines tab.
Configure any settings you wish to have in your Custom Commandline such as the map etc.
Ensure you enable automanagedmods, by clicking the checkbox on both the left and right of this setting.
Here is our knowledgebase on Custom Commandlines.
https://streamline-servers.com/billing/knowledgebase/77/ARK-Custom-Command-lines.html
Step 3: Adding mods to GameUserSettings.ini
Go into your Configuration Files and edit the GameUserSettings.ini
Under the header [ServerSettings] look for the line ActiveMods=
If this line is not here, add it to the config file under the heading [ServerSettings]
Find the mod you want to install from the Steam Workshop.
For example http://steamcommunity.com/sharedfiles/filedetails/?id=485347671
Copy the id="number" for our example it is: 485347671 and add it after ActiveMods=
eg.
ActiveMods=485347671
Add Multiple Mods separated by commas. eg.
ActiveMods=485347671,98649848,39894611
Step 4: Start your service up.
Once you have added the ActiveMods to your GameUserSettings.ini, and if you have automanagedmods enabled in the Game Panel, your service should download and or update these mods from the Steam Workshop when started.
Please note that your service can take several minutes to launch while using automanagedmods, this is due to the service updating mods.