Indeed, it would be useful to tell the reason why you want panels one over another.
Starting with your code, and changing it a lot, I got it to work, but it might not do what you expect...
import java.awt.*;
import javax.swing.*;
public class Test extends JFrame
{
public Test()
{
super();
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
setSize(500, 200);
onInit();
setVisible(true);
}
private void onInit()
{
JLayeredPane lp = getLayeredPane();
JPanel panel = new JPanel();
panel.setLayout(new BorderLayout());
panel.add(new JTextArea(), BorderLayout.CENTER);
panel.add(new JButton("Submit"), BorderLayout.SOUTH);
panel.setSize(300, 150); // Size is needed here, as there is no layout in lp
JPanel glass = new JPanel();
glass.setOpaque(false); // Set to true to see it
glass.setBackground(Color.GREEN);
glass.setSize(300, 150);
glass.setLocation(10, 10);
lp.add(panel, Integer.valueOf(1));
lp.add(glass, Integer.valueOf(2));
}
public static void main(String args[])
{
// Schedule a job for the event-dispatching thread:
// creating and showing this application's GUI.
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
new Test();
}
});
}
}
If totally transparent, well, it is like it isn't here! When opaque, it just covers some of the GUI, but doesn't prevent mouse clicks, for example.