When coding a rich client application in Java SE sooner or later you will have to think about how to lay out your application.

In most cases you will come to the conclusion to lay it out as everyone else does.

1. MenuBar for all functions.
2. ToolBar for more commonly used functions.
3. Controls, which are layed out in a more custom way fitting your needs.

In order to have something ready to start with when I want to lay out the controls of an application I suggest below approach.

Use a BorderPane as root node. In the Top area of a BorderPane you can place a VBox. In this VBox you can place your MenuBar as well as a ToolBar or only a MenuBar.

In the Center area of a BorderPane you can place another layout like a GridPane for high flexibility or a SplitPane to have to separated areas in a BorderPanes Center area.

Enough talk, here is the source as well as an Oracle article that helped me.

MenuBar, ToolBar and Controls in GridPane

import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.geometry.Insets;
import javafx.geometry.Pos;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.Menu;
import javafx.scene.control.MenuBar;
import javafx.scene.control.MenuItem;
import javafx.scene.control.ToolBar;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.GridPane;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class Main extends Application {
	@Override
	public void start(Stage primaryStage) {
		try {
			/* Create a new MenuBar. */
			MenuBar menu = new MenuBar();
			/* Create new sub menus. */
			Menu menuFile = new Menu("File");
			Menu menuHelp = new Menu("Help");
			MenuItem about = new MenuItem("About");
			about.setOnAction(new EventHandler<ActionEvent>() {
				@Override
				public void handle(ActionEvent event) {
					/*
					 * Implement dialog to be prompted when users asks for
					 * details.
					 */
				}
			});
			menuHelp.getItems().add(about);

			/* Adding all sub menus at ones to a MenuBar. */
			menu.getMenus().addAll(menuFile, menuHelp);

			/* Create a button. */
			Button btn = new Button();
			btn.setText("Say Hello World.");
			btn.setOnAction(new EventHandler<ActionEvent>() {
				@Override
				public void handle(ActionEvent event) {
					System.out.println("Hello World!");
				}
			});

			/* Create a new ToolBar. */
			ToolBar tools = new ToolBar(btn);

			/* Create a new VBox and add the menu as well as the tools. */
			VBox menus = new VBox();
			menus.getChildren().addAll(menu, tools);

			/* Create a flexible layout. */
			GridPane contentPane = new GridPane();
			/* Setting the alignment of controls WITHIN a pane. */
			contentPane.setAlignment(Pos.CENTER);
			contentPane.setHgap(10.);
			contentPane.setVgap(10.);
			contentPane.setPadding(new Insets(25, 25, 25, 25));

			/* Create a root node as BorderPane. */
			BorderPane root = new BorderPane();

			/* Adding the menus as well as the content pane to the root node. */
			root.setTop(menus);
			root.setCenter(contentPane);

			/*
			 * Setting the root node of a scene as well as the applications CSS
			 * file. CSS file has to be in same src directory as this class. The
			 * path is always relative.
			 */
			Scene scene = new Scene(root, 800, 600);
			scene.getStylesheets().add(
					getClass().getResource("application.css").toExternalForm());

			/* Adding a scene to the stage. */
			primaryStage.setScene(scene);
			primaryStage.setTitle("FileRex");

			/* Lift the curtain :0). */
			primaryStage.show();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	public static void main(String[] args) {
		launch(args);
	}
}