You have [an image of] a Swing GUI and you want to convert it to JavaFX.
You need a combination of layouts. For the root of the node graph, use a BorderPane.
- The top node is a 
Label but since you want that Label centered, you need to place it in a HBox. 
- The left node is the Bagel pane. The 
RadioButtons are placed in a VBox. 
- The center node is the Toppings pane. The 
CheckBoxes are placed in a VBox. 
- The right node is the Coffee pane. The 
RadioButtons are placed in a VBox. 
- The bottom node contains the 
Buttons. Since you want the Buttons centered, you need to place them in a HBox. 
The below code demonstrates. Note that the code for class BorderedTitledPane comes from the accepted answer to this question: GroupBox / TitledBorder in JavaFX 2?
(Since JavaFX does not have a TitledBorder as Swing does.)
import javafx.application.Application;
import javafx.geometry.Pos;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.CheckBox;
import javafx.scene.control.Label;
import javafx.scene.control.RadioButton;
import javafx.scene.control.ToggleGroup;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.HBox;
import javafx.scene.layout.StackPane;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;
public class OrdaCalc extends Application {
    @Override
    public void start(Stage primaryStage) throws Exception {
        BorderPane root = new BorderPane();
        Label label = new Label("Welcome to Brandi's Bagel House");
        HBox labelHBox = new HBox(label);
        labelHBox.setAlignment(Pos.CENTER);
        root.setTop(labelHBox);
        root.setLeft(createLeftPane());
        root.setCenter(createCenterPane());
        root.setRight(createRightPane());
        root.setBottom(createBottomPane());
        Scene scene = new Scene(root);
        scene.getStylesheets().add(getClass().getResource("application.css").toExternalForm());
        primaryStage.setScene(scene);
        primaryStage.show();
    }
    private HBox createBottomPane() {
        Button calculate = new Button("Calculate");
        Button exit = new Button("Exit");
        HBox buttonsHBox = new HBox(10.0d, calculate, exit);
        buttonsHBox.setAlignment(Pos.CENTER);
        return buttonsHBox;
    }
    private BorderedTitledPane createCenterPane() {
        CheckBox creamCheese = new CheckBox("Cream Cheese");
        CheckBox butter = new CheckBox("Butter");
        CheckBox peachJelly = new CheckBox("Peach Jelly");
        CheckBox blueberryJam = new CheckBox("Blueberry Jam");
        VBox vBox = new VBox(5.0d, creamCheese, butter, peachJelly, blueberryJam);
        BorderedTitledPane center = new BorderedTitledPane("Toppings", vBox);
        return center;
    }
    private BorderedTitledPane createLeftPane() {
        RadioButton white = new RadioButton("White");
        RadioButton wheat = new RadioButton("Wheat");
        ToggleGroup group = new ToggleGroup();
        group.getToggles().addAll(white, wheat);
        VBox vBox = new VBox(30.0d, white, wheat);
        BorderedTitledPane left = new BorderedTitledPane("Bagel", vBox);
        return left;
    }
    private BorderedTitledPane createRightPane() {
        RadioButton none = new RadioButton("None");
        RadioButton regular = new RadioButton("Regular");
        RadioButton decaf = new RadioButton("Decaf");
        RadioButton cappuccino = new RadioButton("Cappuccino");
        ToggleGroup group = new ToggleGroup();
        group.getToggles().addAll(none, regular, decaf, cappuccino);
        VBox vBox = new VBox(5.0d, none, regular, decaf, cappuccino);
        BorderedTitledPane right = new BorderedTitledPane("Coffee", vBox);
        return right;
    }
    public static void main(String[] args) {
        launch(args);
    }
}
class BorderedTitledPane extends StackPane {
    BorderedTitledPane(String titleString, Node content) {
        Label title = new Label(" " + titleString + " ");
        title.getStyleClass().add("bordered-titled-title");
        StackPane.setAlignment(title, Pos.TOP_CENTER);
        StackPane contentPane = new StackPane();
        content.getStyleClass().add("bordered-titled-content");
        contentPane.getChildren().add(content);
        getStyleClass().add("bordered-titled-border");
        getChildren().addAll(title, contentPane);
    }
}
Here is file application.css which is located in the same package as class OrdaCalc.
.bordered-titled-title {
  -fx-background-color: white;
  -fx-translate-y: -16;
}
.bordered-titled-border {
  -fx-content-display: top;
  -fx-border-insets: 20 15 15 15;
  -fx-background-color: white;
  -fx-border-color: black;
  -fx-border-width: 2;
}
.bordered-titled-content {
  -fx-padding: 26 10 10 10;
}
Here is a screen capture.
