In order to add Mods to your Foundry Server you need to do the following:
Stop your Foundry Server
Subscribe to the Mods via the Steam Workshop
Right-click Foundry in your Steam Client
Go to the following directory within that Drive's Steam Folder: "/steamapps/workshop/content/983870"
Select the Mods you want to use - The Individual Mods will be the Folders. The Number of the Folder represents the Steam Workshop ID of the Mod.
Highlight the Mods you want to Install on your Server
Compress the Mods into a .zip Archive
Navigate to the "Files" Tab on the Server Interface and open the "Mods" Folder of your Server ( If it doesn’t exist, create a Mods folder by clicking on “New Directory”)
Upload the .zip Archive containing your Mods using the File Manager
Hover over the uploaded .zip Archive and select the "extract" open within the Context Menu
Start your Server again.