Demonstrates the JavaFX node mouseTransparent and pickOnBounds properties.

LayerClick.java

import javafx.application.Application;
import javafx.beans.binding.Bindings;
import javafx.beans.value.*;
import javafx.scene.*;
import javafx.scene.control.*;
import javafx.scene.layout.*;
import javafx.scene.paint.Color;
import javafx.scene.shape.*;
import javafx.stage.Stage;

// Demonstrates the JavaFX node mouseTransparent and pickOnBounds properties.
public class LayerClick extends Application {
  public static void main(String[] args) { launch(args); }
  @Override public void start(Stage stage) throws Exception {
    ToggleButton testButton = new ToggleButton("");
    
    VBox layer1 = new VBox();
    layer1.getChildren().add(testButton);

    Node layer2 = new Circle(100, 100, 100, Color.FIREBRICK);
    layer2.setOpacity(0.7);

    StackPane stack = new StackPane();
    stack.getChildren().setAll(layer1, layer2);    
    stack.setStyle("-fx-background-color: azure;");
    
    VBox layout = new VBox();
    layout.getChildren().setAll(
            stack, 
            createControls(testButton, layer2)
    );
    
    stage.setScene(new Scene(layout));
    stage.show();
  }

  private VBox createControls(ToggleButton controlledButton, Node controlledNode) {
    controlledButton.textProperty().bind(
            Bindings
              .when(controlledNode.mouseTransparentProperty()).then("Completely Clickable")
              .otherwise(Bindings
                 .when(controlledNode.pickOnBoundsProperty()).then("Not Clickable")
                 .otherwise("Partially clickable")
              )
    );
    
    CheckBox enableMouseTransparency = new CheckBox("Enable MouseTransparency");
    enableMouseTransparency.setSelected(controlledNode.isMouseTransparent());
    controlledNode.mouseTransparentProperty().bind(enableMouseTransparency.selectedProperty());
            
    CheckBox enablePickOnBounds      = new CheckBox("Enable Pick On Bounds");
    enablePickOnBounds.setSelected(controlledNode.isPickOnBounds());
    controlledNode.pickOnBoundsProperty().bind(enablePickOnBounds.selectedProperty());

    VBox controls = new VBox(10);
    controls.setStyle("-fx-background-color: cornsilk; -fx-padding: 10;");
    controls.getChildren().addAll(
            enableMouseTransparency,
            enablePickOnBounds
    );
    
    return controls;
  }
}

Answer to the Oracle JavaFX forum question: Best approach to manage overlay node?