Спасибо всем за помощь. Я нашел способ сделать это, используя GridPane (root панель), VBox, Anchor и панели стека. , Вот f xml для этого
<?xml version="1.0" encoding="UTF-8"?>
<?import javafx.scene.control.ScrollPane?>
<?import javafx.scene.effect.DropShadow?>
<?import javafx.scene.layout.AnchorPane?>
<?import javafx.scene.layout.ColumnConstraints?>
<?import javafx.scene.layout.GridPane?>
<?import javafx.scene.layout.RowConstraints?>
<?import javafx.scene.layout.StackPane?>
<?import javafx.scene.layout.VBox?>
<ScrollPane fitToHeight="true" fitToWidth="true" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" xmlns="http://javafx.com/javafx/11.0.1" xmlns:fx="http://javafx.com/fxml/1">
<content>
<GridPane hgap="10.0" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" minHeight="700.0" minWidth="700.0" style="-fx-border-width: 20px; -fx-border-color: white;">
<columnConstraints>
<ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
<ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
<ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
</columnConstraints>
<rowConstraints>
<RowConstraints maxHeight="347.79999389648435" minHeight="10.0" prefHeight="139.0000061035156" vgrow="SOMETIMES" />
<RowConstraints maxHeight="309.79999389648435" minHeight="10.0" prefHeight="180.00003662109373" vgrow="SOMETIMES" />
<RowConstraints maxHeight="204.79996337890628" minHeight="10.0" prefHeight="204.79996337890628" vgrow="SOMETIMES" />
</rowConstraints>
<children>
<VBox prefHeight="479.0" prefWidth="274.0" spacing="10.0" style="-fx-background-color: blue; -fx-border-insets: 10;" GridPane.rowSpan="2147483647">
<effect>
<DropShadow />
</effect>
</VBox>
<VBox prefHeight="200.0" prefWidth="100.0" spacing="10.0" GridPane.columnIndex="1" GridPane.columnSpan="2147483647" GridPane.rowSpan="2147483647">
<children>
<AnchorPane prefHeight="178.0" prefWidth="547.0" style="-fx-background-color: green;">
<effect>
<DropShadow />
</effect>
</AnchorPane>
<StackPane maxHeight="1.7976931348623157E308" prefHeight="403.0" prefWidth="547.0" style="-fx-background-color: yellow;" VBox.vgrow="ALWAYS">
<effect>
<DropShadow />
</effect>
</StackPane>
</children>
</VBox>
</children>
</GridPane>
</content>
</ScrollPane>
Один, который я добавил, это моя пограничная панель, вот как это выглядело
![enter image description here](https://i.stack.imgur.com/ggAar.png)