I'm going to assume you know the basics of turning a dedicated server on. If not, read this guide first:

https://eah.empyrion-homeworld.net/documentation/first-steps/quickstart


You need to copy the mod folder from Steam Workshop's folder to the scenario folder for the Dedicated Server.

Assuming you use default install locations:

Create a folder here inside the Scenarios folderfor the mod files to go:

C:\Program Files (x86)\Steam\steamapps\common\Empyrion - Dedicated Server\Content\Scenarios

Go to
C:\Program Files (x86)\Steam\steamapps\workshop\content\383120\314322581

Copy everything inside this folder to the folder you created in Scenarios.

After you do all of this, you can select the scenario in Empyrion Admin Helper(shown in second screenshot in guide)