Method One: Web console
Login to your server's control panel and navigate to your server.
Start the server and allow it to fully load up
Once it has started up, click on the Web Console icon in the control panel.
Run the command: /moddb install ModID
The ModID will usually be the name of the mod without any spaces. It will usually be the name shown in the URL of the mod
Example
https://mods.vintagestory.at/primitivesurvival
The ModID for the mod would be primitivesurvival
You would run the command: /moddb install primitivesurvival
Method Two: Manual mod upload
Upload the mod's .zip file to the Mods folder on the server using either the File Manager option in the server's control panel or using an FTP client
https://hosthavoc.com/billing/knowledgebase/522/How-to-use-an-FTP-client-with-your-Vintage-Story-service.html