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Building a JFrame that run in the same order in Java

I'm making a JFrame that contains a lot of JButtons and JTextfields which contain data from a database. In the design everything is okay, but when I run my program the JButton and the JTextfield change their places and I don't know why.
Here is a screen shot from the design window and the run window:

Seems like you have aligned the textfields to each other and the buttons too. But you should have aligned one button to one textfield. One way to do this would be to use a GridBagLayout instead of the FreeDesign option in NetBeans. To do this right-click onto your frame and select Set Layout>Grid Bag Layout.
You can then right-click again and select Customize Layout... in order to place your components as you wish.

NetBeans - How to show all Swing components in a JFrame?

I'm making a Swing GUI with NetBeans, using the built-in form maker, which works quite well.
However, if I accidentally put the wrong panel on a form, I have no way to delete it, or select it again.
Likewise, if I want a button to open a new window, say, a file chooser, I don't know how to add that file chooser to the form, but not have it appear until the button is pressed.
Does anyone have any experience with the NetBeans Swing form builder? This seems like a common thing to have to do, but I don't see how to do it. Am I missing something?

Yay a netbeans user!Yea there should be a navigator window in the bottom left corner. There it displays all of the components on the form. Im not too sure what you mean by a file chooser, but to open a new window,ie another Jform, you create another form class. Then you create that form and setVisible.
So lets say you have
a form mainProgram
And form helpMenu
In the mainProgram
public mainProgram(){
InitComponents();//or something on the lines of that
helpMenu helpMenuWindow = new helpMenuWindow();
helpMenu.setVisible(true);
}
This will allow you to be able to open new windows, but if you click on the red X to close the window, it closes your whole program. In properties for the helpMenu pane you can select the option for what the window should do on exit.
Exit
Hide
Do nothing
In the code above is the code that is run before the Jpane displays, if you want to show or hide items, just code
Object.setVisible(boolean);
I hope I answered your question Tetramputechture.

The proper way to change content in a Java GUI application (not creating a new window each time)?

I need to make a Java desktop application for a client and the last time I did Java it was 2 years ago and a little odd.
My main query is regarding navigation between GUI.
In the past, I would just create a new JForm (JFrame maybe?) whenever a button was pressed and a new GUI form/window would open up.
This time, I'd like the GUI to be inside one JForm/JFrame with just the inner content changing, how most applications look when you press a button.
I assume this is done by putting all of my GUI elements in JPanels, and deleting/creating them when buttons are pressed on the same JForm?
If not how do I do it properly?
I'll also be using Netbeans GUI editor, if anyone has a better alternative for a Java GUI builder/IDE, let me know.
Thanks!

The simplest approach would be to use a CardLayout
This will allow you to add multiple components to the UI and control which one is actively visible

Another approach could be to create menus and menuItem and having multiple JFrames now you can get the same JFrame to be displayed whenever you click the same menuItme button. This way You can minimize the creation of JFrames.

How to put JFrame into existing JPanel in Java Swing?

I have an open-source java swing application like this:
http://i47.tinypic.com/dff4f7.jpg
You can see in the screenshot, there is a JPanel divided into two area, left and right area. The left area has many text links. When I click the SLA Criteria link, it will pop-up the SLA Criteria window. The pop-up window is JFrame object.
Now, I'm trying to put the pop-up window into right area of the JPanel, so that means no pop-up window anymore, i.e. when I click the SLA Criteria link, its contents will be displayed at the right area of the JPanel. The existing content of the right area of JPanel will not be used anymore. The concept is just same like in the java api documentation page: http://docs.oracle.com/javase/6/docs/api. You click the link in the left frame, you'll get the content displayed at the right frame.
The example illustration is like this:
(note: it's made and edited using image editor, this is not a real screenshot of working application)
http://i48.tinypic.com/5vrxaa.jpg
So, I would like to know is there a way to put JFrame into JPanel?
I'm thinking of using JInternalFrame, is it possible? Or is there another way?
UPDATE:
Source code:
http://pastebin.com/tiqRbWP8 (VTreePanel.java, this is the panel with left & right area divisions)
http://pastebin.com/330z3yuT (CPanel.java, this is the superclass of VTreePanel and also subclass from JPanel)
http://pastebin.com/MkNsbtjh (AWindow.java, this is the pop-up window)
http://pastebin.com/2rsppQeE (CFrame.java, this is the superclass of AWindow and also subclass from JFrame)

Instead of trying to embed the frame, you want to embed the frame's content.
There is (at least) one issue I can see with this.
The menu bar is controlled by the frame's RootPane.
Create you're self a new JPanel. Set it's layout to BorderLayout.
Get the menu bar from the frame (using JFrame#getJMenuBar) and added to the north position of you new panel.
Get the frames ContentPane and add it to the center position of the panel.
There is undoubtedly countless other, application specific issues you will run into trying to do this...

No, you don't want to "put a JFrame into a JPanel" and your illustration above doesn't demonstrate this either. Instead it's showing a subordinate window on top of (not inside of) another window. If you absolutely need to display a new subordinate window, I'd recommend that you create and display a JDialog. The tutorials will explain how to do this, or if you get stuck post your code attempt and we'll help you work with this.
Edit 1
You state:
I need to convert from the pop-up window style into the jpanel content style. It's just like the java api documentation page style: docs.oracle.com/javase/6/docs/api When you click the text in left frame, it doesn't show any pop-up, right? The content is displayed at right frame directly. So that's basicly my goal. The source code is quite big. I will try to paste the source code if possible.
What you are looking for is to simply implement a MouseListener in a JList or JTable, and when responding to the click get the content based on the selection made. This has nothing to do with placing a JFrame in a JPanel and all to do with writing the correct program logic. Again, display it in a modal JDialog -- but that's all secondary to your writing the correct non-GUI logic. You're really barking up the wrong tree here. Forget about JFrames, forget about JPanels for the moment and instead concentrate on how you're going to extract the SLA Criteria data when it is clicked on.
Edit 2
I think I see what you're trying to do -- instead of JFrames and JDialogs, use JPanels and swap them using a CardLayout which would allow you to swap views.

I had skimming the source codes, I saw that the AWindow.java has internal panel (APanel.java) to hold the window's content, and it also has a public method to return the content panel object (getAPanel()). With this, I can use it for fetching the window's contents into other container.
Finally, I decided to use JTabbedPane in the right area of VTreePanel for displaying the pop-up window's contents.

You cannot put a Jframe into a JPanel. Instead you should try to create a separate panel that has functionalities like your JFrame and embed that into your JPanel.
Since you can put a JPanel into another JPanel but not a JFrame into another JPanel

Removing JPanel from a JFrame in NetBeans

I have several JPanels that contain buttons, labels, etc. that I want to switch between from a main JFrame. Currently I am trying to use the this.add(JPanelname); method and this.remove(JPanelname); with the validate(); and repaint(); methods
The problem is it will add the panel to the JFrame but it will not remove it. I am not sure how exactly to go about this.

Maybe you should be using a Card Layout.
Or maybe you should be using modal JDialogs. So whenever you click on the "widjet" a new window is displayed. Then when you close the dialog you are back on your main frame.

If you are constantly switching between JPanels, then a JTabbedPane may be the right thing to use. It should not be necessary to call "validate" or "repaint" when you add or remove a JPanel. Do you have a layout manager installed? Do you make sure to call add/remove only within the UI event thread? Also, typically one does not call "validate()" but rather "invalidate()" to invalidate the container for updates.