datadirectory, copy the example files, then and customise them to your requirements.
serverfilesdirectory and run the Factorio binary.
Map, then adjust options accordingly. Doing so will generate a file called
mod-settings.datwhich stores these settings.
mod-settings.datfile to your server with a tool like Filezilla or the
rsynccommand on Mac/Linux, or even a USB drive.
rsync, the command would look something like this:
serverfiles/modsdirectory. You will also need to delete the existing save so that it generates a new one with the new generation rules. (This is a great time to make backups if you have any progress you would like to save).