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JAVA - How do I make the user be able to utilize only the frame on top?

When two JFrames are enabled, I want the user to be able to use only one in the top (think of that like an error pop up on your screen, when you can't press anything but the popup itself). I am aware of the class JInternalFrame and I chose not to use it for my program. Thanks in advance :)

Use JDialog, you can set your main frame as the JDialog's parent frame, so that whenever your main frame and JDialog will display, you will be able to click only the JDialog, not your main frame.

You want a modal behaviour, then. I think you can try using JDialog instead of JFrame, something like:
JDialog dialog = new JDialog(parentFrame, title, true); //parameters: owner, title and modal
dialog.getContentPane().add(somePanel);
dialog.pack();
dialog.setVisible(true);
You can read more about it here: http://docs.oracle.com/javase/tutorial/uiswing/misc/modality.html

Java Swing: JOptionPane appears by itself without parent window when restored?

I have a JOptionPane which appears on top of it's parent JFrame window, but when the application is minimized and restored, only the JOptionPane will show and not the parent JFrame.
How to fix this bug?

JOptionPane is a modal dialog box.
It means first you need to handle/close this dialog box then you will be able to access your main window.
So when you minimize everything and then restore it, it firstly shows the JOptionPane when you will close it or what it is supposed to do ONLY then you will get the main window.
It's not a bug. It is just how modal things work.
You will not be able to even Minimize the main window from icon when JOptionPane is up. You can minimize everything like with Window + D key or Window + M key in Windows PCs.

Restrict Access to other JFrame

How do i restrict access to other JFrame?
if I open my main frame and when click the button to display other jframe, the user should not be able to go back to the main frame.
how do I do that?

if i open my main frame and click the add button,
When you click the button you display a modal JDialog. Then until the user closes the dialog they won't be able to access the main frame.

try this method...
this.setEnabled(false);

Your question is not clear to me but as per my understanding I believe You want to open a dialog on button click but when you click the button a new JFrame is displayed and it becomes impossible for you to get back to the original frame.
Use a dialog /pop-up on your button click like JOptionPane.
If you want to open a JFrame on button click, making a HOME button on the newly created/opened JFrame and linking that button to main JFrame might be a good option.Closing the newly created JFrame will display the originally created JFrame anyway.

Use a dialog (JDialog class) instead and make it modal.
Here is some help on how to do this:
http://download.oracle.com/javase/tutorial/uiswing/components/dialog.html
Regards,

How to make a resizable JDialog?

I'm using JOptionPane.showOptionDialog to show a JDialog. I would like to know how:
set the dimension of the dialog (for now I'm using setPreferredSize() method on the given panel but I know that such method shouldn't be used).
make the showed dialog resizable.
My code looks like:
JPanel panel; //my JPanel built with dialog contents
int ret = JOptionPane.showOptionDialog(myFrame,
panel,
"titel",
JOptionPane.YES_NO_OPTION,
JOptionPane.PLAIN_MESSAGE,
null,
options,
options[1]);
I know that I could obtain the desired result building a JDialog this way:
JDialog dialog = new JDialog(panel);
dialog.setResizable(true);
dialog.setSize(800,600);
dialog.setVisible(true);
The problem with the last solution is that I can't get the return value.
EDIT:
in response to #camickr observations:
Why do you need to set the preferred size? If you build the panel
properly is should be displayed at its preferred size.
I'm not sure of having fully understood Swing on this point. The problem is, for example, that I'm displaying through a JDialog a ChartPanel built with JFreeChart. Now, I suppose that panel has it's own preferred size, but I want to see it bigger. How can I do that without explicitly use setPreferredSize()?
Read the JOptionPane API. Search for "Direct Use". It shows you how to
directly access the dialog used by the option pane and you can
I read it but I can't find the right method to understand which button (Ok or Cancel) has been pressed on the JDialog.

This hack using a HierarchyListener to get access to the JOptionPane's also works:
http://blogs.oracle.com/scblog/entry/tip_making_joptionpane_dialog_resizable
// TIP: Make the JOptionPane resizable using the HierarchyListener
pane.addHierarchyListener(new HierarchyListener() {
public void hierarchyChanged(HierarchyEvent e) {
Window window = SwingUtilities.getWindowAncestor(pane);
if (window instanceof Dialog) {
Dialog dialog = (Dialog)window;
if (!dialog.isResizable()) {
dialog.setResizable(true);
}
}
}
});

Why do you need to set the preferred size? If you build the panel properly is should be displayed at its preferred size.
Read the JOptionPane API. Search for "Direct Use". It shows you how to directly access the dialog used by the option pane and you can
With you second approach why are you setting the size? Again just pack() the dialog and it will be displayed at the panels preferred size.
What do you mean you can't get the return value? You have access to any method of your custom panel. So you can just invoke the getXXX() method when you receive control again. Just make sure the dialog is modal and the code after the setVisible(true) will block until the dialog is closed.

If you want to go the second way completely, you have to create and position your own "YES" and "NO" buttons somewhere (since a raw JDialog is just an empty modable frame). Therefore, you need to attach a MouseListener to both buttons and handle click events. On a click, you will know what button was pressed, and you'll just have to call dispose() on the dialog to close it.

How do I make dynamic windows in Swing?

I have a general question. I would like to have a window containing some buttons, radio buttons, text fields and so on. So, user can do something (write text, select options and press buttons). As the result of the user activity window should change it structure/appearance some element should disappear and some appear.
How do I program such "updates"? Should I close an old window and open a new one or I can modify content of window without closing it?

After adding your components or such, calling revalidate() on your container will do the updates