Minecraft: Java Edition is stored in the ./home/minecraft/mc-instances/mc-INSTANCEIDHERE/ directory, it can be accessed via the Files menu for your game instance, or, sFTP/SSH. Files added to the instance's directory will be detected by the control panel and software utilizing them.
The instance ID is in your browser URL, eg: "panel.creeper.host/TestServer/services/mc/mc-5c604c6ddc398/files" when visiting any submenu for that instance.
Uploading files using the 'root' login details for SSH/sFTP may cause problems with the control panel being able to access files/folders. Where possible, always login using the standard 'minecraft' level key.
An example of a healthy structure listing (Note: "Files" menu does not show the /home/minecraft/* part of the file structure):
Any files dropped into the /home/minecraft/ directory via sFTP/SSH will not be detected by the instances sub-menus, they must be within the /home/minecraft/mc-instances/mc-INSTANCEIDHERE/ directory.