While I'm not sure what you want the final result to look like, here's a few of my suggestions.
In the snippet where you add the warning panel to the JFrame
warningPanel.add(warningLabel);
contentPane.add(warningPanel);
pack();
contentPane being the container returned by JFrame.getContentPane()
JFrames by default use the BorderLayout, and so,
contentPane.add(<someComponent>)
is identical to
contentPane.add(<someComponent>, BorderLayout.CENTER)
You also add the mainPanel the same way, and you can't have two components with the same constraints, so instead set the warningPanel to BorderLayout.NORTH
contentPane.add(warningPanel, BorderLayout.NORTH)
And also remove the call to pack() in that code snippet, since you call it later on in your code.
Hope this helps.
PS
As for GUI building in Eclipse, this previous question on Eclipse GUI Builder plugins maybe of use. I can't speak for tutorials on using Swing in Eclipse, but a quick google search digs up this tutorial using the Eclipse Visual Editor project