I'll preface this by saying that there's probably an easier way to do this, but this is what works for me. I'll be using my setup as an example, but this should work on any setup though the file paths may be different.
What you'll need:
Atlas (obviously, preferably on steam)
Filezilla or your prefered ftp client
Mod id's for the mods you want to use (these can be found on the steam mod page, in the browser address, it's all the #'s after id= )
FTP Host name, user name, password, and port for each server (on nitrado, these are found at the bottom left of each server's dashboard page)
1. Subscribe to the mods you'd like to use on steam.
2. Launch Atlas to force steam to download your selected mods.
3. Close Atlas.
4. Launch Filezilla.
5. In the appropriate fields enter the host name, user name, password, and port for your home server and hit enter.
6. On the left side, navigate to your desktop (c:\users\desktop)
7. On the right side navigate to atlasmain\shootergame\saved\savegame*\config\WindowsServer (*the savegame folder will have a long string of numbers\letters for a name, if there's more than one, use the one with the most recent time stamp)
8. Drag the GameUserSettings.ini file over to the desktop folder on the left.
9. Open the GameUserSettings.ini file you just downloaded with a text editor (notepad, etc.).
10. At the bottom of the server settings section (the first section, before [/Script/ShooterGame.ShooterGameUserSettings]) add ActiveMods= followed by your mod id's separated by a comma (for example ActiveMods=1629667379,1629097213,1628157075,1635287345,1633503401) in the order you want them to be loaded.
11. Save and close GameUserSettings.ini
12. Copy GameUserSettings.ini back to your server.
13. On the left side navigate to your atlas content folder (c:\program files x86\steam\steamapps\common\atlas\shootergame\content
14. On the right side navigate to atlasmain\shootergame\content (you will need to create the content folder if it isn't there already).
15. Drag the mods folder from the content folder on the left to the one on the right and wait until filezilla tells you that the transfer is complete.
16. Repeat 12-15 for each of your expansion servers using their hostname, user name, password, and port (each one is different on nitrado), on expansion servers the filepath will start in atlasexp instead of atlasmain but is otherwise the same.
17. Once you've completed uploading the files, close filezilla, restart your cluster, log in, and enjoy modded goodness =D