You can make any Pane "mouse transparent", so that it doesn't consume any click events, and lets them pass through to the stack under it.
Here's some example code... this example sets up 4 panes in a stack, with just the mainPane accepting clicks to begin with.
StackPane rootPane = new StackPane();
VBox mainPane = new VBox(80);
BorderPane helpOverlayPane = new BorderPane();
helpOverlayPane.setMouseTransparent(true);
Canvas fullScreenOverlayCanvas = new Canvas();
fullScreenOverlayCanvas.setMouseTransparent(true);
VBox debugPane = new VBox();
debugPane.setAlignment(Pos.BASELINE_RIGHT);
AnchorPane debugOverlay = new AnchorPane();
debugOverlay.setMouseTransparent(true);
debugOverlay.getChildren().add(debugPane);
AnchorPane.setBottomAnchor(debugPane, 80.0);
AnchorPane.setRightAnchor(debugPane, 20.0);
rootPane.getChildren().addAll(mainPane, fullScreenOverlayCanvas, debugOverlay, helpOverlayPane);
Now, when you want to use your canvas to draw on top, make sure you change mouse transparent to false for just that stack, and keep all panes on top of it mouse transparent.
fullScreenOverlayCanvas.setMouseTransparent(false);
debugOverlay.setMouseTransparent(true);
fullScreenOverlayCanvas.setVisible(true);
doSomethingWithCanvasThatNeedsMouseClicks();
P.S. I did some editing of the code I had, so it may not run as-is. Also, see discussion of making only parts of panes transparent here:
JavaFX Pass MouseEvents through Transparent Node to Children