Hi, am not sure if my answer is correct or simply basic, when I installed mods as I was told to do from Nitrado support, was get the MOD ID number and under the atlas configuration of the main server I put the mod ID after switching off the server, save it, then restart the server, when next time you launch the game it will download all the needed files, just make sure you subscribed to all the mods, I made the mistake that I added the MOD ID but forgot to subscribe.
I don't know and am not sure I answered your question. If not, hopefully someone can provide a more appropriate answer.
Regards.