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Java GUI layout questions

Sorry if this has been posted before, but I cannot seem to find any good info that helps me, or I just don't understand other answers enough to help me as I just started programming GUIS.
I wrote a program that has various Items in their own (sub)Jpanel(jtextfields. combobox's, buttons etc.) and all the sub Jpanels in a main jpanel inside a jframe. My goal is to center and stack each sub JPanel on top of one another, so that when the user resizes the window each item stays centered and stacked on top of one another. (when I stacked I don't mean layered where one pane is in front of another, rather stacking the panes like a sandwich so to speak) My panes just move with the default flowlayout and I hope to stop that.
I have seen BoxLayout but like I said, I am new to GUIS and I am not sure if I can apply the BoxLayout to Jpanels.

First off, what you're referring to is a JPanel, not a JPane
Secondly,
JPanel panel = new JPanel(new BorderLayout());
BorderLayout is probably your best bet. For more information on layouts, check out
http://docs.oracle.com/javase/tutorial/uiswing/layout/using.html#choosing
And by the way, NetBeans GUI Builder is probably your best friend as an introductory GUI programmer.

There are easy ways to design your User Interface in Java Swing or the last One JAVAFX. In Swing, there is a eclipse plugin called Swing Windows Builder, there you can easily build your UI by dragging and dropping and As for the JAVAFX, there is Nice and free IDE called Intelli IDE CE, it has also built-in UI designer called Oracle JavaFx Scene Builder. Go for the JavaFx and speed up your development.

Swing JScrollPane resets scroll position when updating

I have a JPanel view inside a JScrollPane. The Jpanel paints some shapes which has to change dynamically in order to reflect a changing datamodel.
I have implemented a timer that should repaint the JPanel/JScrollPane which works fine unless that it resets the scroller. The scroller has to remain at its position (where the user has scrolled to).
I have tried to repaint the JPanel, the JScrollPane, the viewport of the JScrollPane etc, but noting seem to solve this problem.
Do you have a hint? The code is quite large so it is hard to isolate an example.

On the swing timer do not much concerning the GUI, just scrollPane.repaint(50L);. Especially refrain where not needed from layouting calls: (in)validate.

I have now isolated the code only to find out that it works isolated. It seem to be related to the context (a very complex form) that it is put in. Now a SSCCE is completely impossible, but any input is still appreciated.

Resizing a JPanel inside a JFrame

I am new to Java, started learning swing and have a problem with resizing a JPanel inside a JFrame. I am following this tutorial:
http://vincentramdhanie.blogspot.com/2009/11/cardlayout-with-netbeans.html
because ultimately I am learning each of the different layouts and have come to the CardLayout now. In the above, there is a JPanel being used for a status panel. That is what I want to do as well, but when I drag a JPanel onto my blank JForm it takes up all the space and I don't see any resizing handles for it like I would if I were using a .NET panel. Changing preferredSize in the properties window also does nothing. What am I missing here? I feel like a complete noob for asking such a basic question but I really can't find any way to resize this thing.. :-|
EDIT:
I forgot to mention; I am using NetBeans IDE

You can't resize the JComponent because you've select CardLayout. The CardLayout can holds/manages one or more components that share the same display space.
What you need to read documentation and good tutorials.

How to resize controls at runtime in java

Is there a way to resize a control, a JTextfield for example, at runtime in java? I want my textfield to have the resize cursors (just like when you point your cursor on the corner of a window) and will be able to resize on runtime. Ive read on the internet that vb6 and C# have those capabilities, is there anything for java? A sample code or a link to a good tutorial will be very much appreciated. Thank you.

It sounds like you are trying to implement a component editor, such as the GUI editors available in popular programing IDEs. The essential feature is a handle, a graphical object that can be selected and dragged to change the geometry. GraphPanel is a simple example of an object drawing program that illustrates many of the required techniques.

That depends on the Layout of the JTextField's container. A good tutorial is available at http://docs.oracle.com/javase/tutorial/uiswing/layout/visual.html

For a quick and cheap solution you could use a JSplitPane component, with the JTextField to be resized in the left side, and an empty JPanel in the right side. By default a JSplitPane is decorated with a border and a divider, but you can remove these by setting an empty border.

Veil LoadingImage or LoadingPanel over JFrame

Is there any component in Swing(X) by which we can place a veil loading image over a panel or frame making it transparent during some lengthy background processing?

Few examples of Romain Guy's work:
Chapter 9 of “Filthy Rich Clients” book, with downloadable code
SwingFX: Pretty Progress Panels
Glasspane Painting
GlassPane Intercepts
And other example:
GlassExample

You're looking for the Glass Pane, work through the tutorial here and the relevant section here

You need to add a glasspane to the frame, thats right. But you also can use SwingX' JXFrame and simply set a waitpane and activate it when a loading action starts.
Have a look at the API