Example java class in creating multiple config files on bukkit.

MultipleDataFiles.java

package me.ruptur.multipledatafiles;

import java.io.File;
import java.io.IOException;
import java.util.logging.Level;

import org.bukkit.Bukkit;
import org.bukkit.configuration.file.FileConfiguration;
import org.bukkit.configuration.file.YamlConfiguration;
import org.bukkit.entity.Player;
import org.bukkit.event.EventHandler;
import org.bukkit.event.Listener;
import org.bukkit.event.player.PlayerJoinEvent;
import org.bukkit.plugin.Plugin;
import org.bukkit.plugin.java.JavaPlugin;

public class MultipleDataFiles extends JavaPlugin implements Listener{

	private Plugin plugin;
	
	private File datafile;
	private FileConfiguration data;
	private File playerfile;
	private FileConfiguration player;
	
	public void onEnable() {
		this.plugin = this;
		
		this.getServer().getPluginManager().registerEvents(this, this);
		
		try {
			getFiles();
		} catch (IOException ex) {
			log(Level.SEVERE, "[MultipleDataFiles] Was unable to create files!");
			log(Level.INFO, "[MultipleDataFiles] Delete data file and try again");
			this.plugin.getPluginLoader().disablePlugin(this.plugin);
		}
		
		for (Player p : this.getServer().getOnlinePlayers()) {
			loadPlayer(p.getName());
		}
	}

	@EventHandler 
	public void onJoin(PlayerJoinEvent e) {
		loadPlayer(e.getPlayer().getName());
	}
	private void loadPlayer(String name) {
		setValue(player, name + ".name", name);
		
		if (data.getInt("loaded count") == 0) {
			setValue(data, "loaded count", 0);
		}
		
		setValue(data, "loaded count", data.getInt("loaded count") + 1);
	}

	private void getFiles() throws IOException {
		if (!plugin.getDataFolder().exists) plugin.getDataFolder().mkdir();
		datafile = new File(plugin.getDataFolder(), "data.yml");
		playerfile = new File(plugin.getDataFolder(), "players.yml");

		if (!datafile.exists()) datafile.createNewFile();
		if (!playerfile.exists()) playerfile.createNewFile();
		
		data = YamlConfiguration.loadConfiguration(datafile);
		player = YamlConfiguration.loadConfiguration(playerfile);
		
	}


	private void log(Level level, String message) {
		Bukkit.getLogger().log(level, message);
	}
	
	private void setValue(FileConfiguration c, String path, Object value) {
		c.set(path, value);
		trysave(c);
	}
	
	private void trysave(FileConfiguration c) {
		try {
			c.save(file(c));
		} catch (IOException e) {
			log(Level.SEVERE, "[MultipleDataFiles] Was unable to save "  + c.getName() + " file");
		}
	}
	private File file(FileConfiguration c) {
		return c.getKeys(false) == YamlConfiguration.loadConfiguration(datafile) ? datafile : playerfile;
	}
}