Пожалуйста, изучите образец. Обратите внимание на атрибуты min_width, min_height, pref_width, pref_height, max_width, max_height, vgrow, hgrow в SceneBuiler. Основная концепция заключается в том, что используемый вами тип панели дает вам желаемое расположение. Это не должно быть жестко закодировано.
<?xml version="1.0" encoding="UTF-8"?>
<?import javafx.geometry.Insets?>
<?import javafx.scene.control.Button?>
<?import javafx.scene.control.Label?>
<?import javafx.scene.control.TextField?>
<?import javafx.scene.layout.ColumnConstraints?>
<?import javafx.scene.layout.GridPane?>
<?import javafx.scene.layout.HBox?>
<?import javafx.scene.layout.RowConstraints?>
<?import javafx.scene.layout.StackPane?>
<?import javafx.scene.layout.VBox?>
<HBox maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.171" xmlns:fx="http://javafx.com/fxml/1">
<children>
<VBox style="-fx-background-color: yellow;">
<children>
<StackPane VBox.vgrow="ALWAYS">
<children>
<Button mnemonicParsing="false" text="Menu Button" />
</children>
</StackPane>
<StackPane VBox.vgrow="ALWAYS">
<children>
<Button mnemonicParsing="false" text="Menu Button" />
</children>
</StackPane>
<StackPane layoutX="10.0" layoutY="210.0" VBox.vgrow="ALWAYS">
<children>
<Button mnemonicParsing="false" text="Menu Button" />
</children>
</StackPane>
<StackPane layoutX="10.0" layoutY="276.0" VBox.vgrow="ALWAYS">
<children>
<Button mnemonicParsing="false" text="Menu Button" />
</children>
<VBox.margin>
<Insets />
</VBox.margin>
</StackPane>
<StackPane layoutX="10.0" layoutY="310.0" VBox.vgrow="ALWAYS">
<children>
<Button mnemonicParsing="false" text="Menu Button" />
</children>
</StackPane>
</children>
</VBox>
<VBox style="-fx-background-color: red;" HBox.hgrow="ALWAYS">
<children>
<StackPane prefHeight="150.0" prefWidth="200.0" style="-fx-background-color: green;" VBox.vgrow="ALWAYS">
<children>
<GridPane maxHeight="-Infinity" maxWidth="-Infinity" style="-fx-background-color: purple;">
<columnConstraints>
<ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
<ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />
</columnConstraints>
<rowConstraints>
<RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
<RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
<RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
</rowConstraints>
<children>
<Label text="Label" />
<TextField GridPane.columnIndex="1" />
<TextField GridPane.columnIndex="1" GridPane.rowIndex="1" />
<TextField GridPane.columnIndex="1" GridPane.rowIndex="2" />
<Label text="Label" GridPane.rowIndex="1" />
<Label text="Label" GridPane.rowIndex="2" />
</children>
</GridPane>
</children>
</StackPane>
<HBox alignment="TOP_RIGHT">
<children>
<Button mnemonicParsing="false" text="Button" />
</children>
</HBox>
</children>
</VBox>
</children>
</HBox>