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Java FX Multiple Windows App

How are big applications (with lots of windows, lets say users administration, roles, payments, etc) designed. I'm a web developer and I'm used to develop different screens in different html files. I wanna know how to split windows generations in different files instead of having only one huge Application class.
Thanks in advance..

The question is a bit too broad to thoroughly answer, but I still think providing a partial answer here might be useful.
For an implementation of Banislav's strategy of hyperlinks controlling a swappable pane (which does not use FXML), see the related question: How to have menus in java desktop application.
For a small FXML based framework for switching panes see: Loading new fxml in the same scene with associated sample code. Note that sample is for small apps, for large apps a more rigorous framework would be preferred.
The next step up from the small framework listed above would be something like afterburner.fx, which is "a minimalistic (3 classes) JavaFX MVP framework". Even though small, afterburner.fx would probably suffice to be used as the core for a medium sized application. You can find a small sample application built using afterburner.fx named airhacks-control.
For something a bit more involved you can study the source of SceneBuilder and SceneBuilderKit. SceneBuilder is an open source design tool written in JavaFX. Understanding and adapting that code may be challenging for somebody coming from a web background as its implementation differs significantly from a traditional web application.
For very large applications, basing the application on a fully featured platform such as NetBeans RCP would probably be a preferred approach, though, as of this time, that is probably a large and difficult task to do well and likely requires mixing multiple frameworks rather than writing everything purely in JavaFX.

In JavaFX, you can use similar approach as in web development.
Use BorderPane as root pane.
Create main menu
You can use MenuBar with Menus and MenuItems. You can also use TreeView or ListView on like left side of screen. To position TreeView/ListView on left side you could use BorderPane and set it to left with setLeft.
Approach I prefer would be to use HyperLink control. Add multiple HyperLink's to VBox and again, set them on left side of BorderPane. Upon click, they will handle event which set's desired form on center of BorderPane.
I.e.

Mixing Swing and JavaFX in a Java desktop chat application

I know that there are already some question about this, but I can't find my way!
I want to implement a desktop chat application with java which is able to send text,image, video, etc.
Now I am using swing component for my chat conversation window.
I create a JFrame and add JTabbedPane to it inorder to have tab for each new conversation.
for creating each tab I act as follow :
create JPanel (I add this to my JTabbedPane as tab)
newtab = new JPanel();
newtab.setLayout(new BoxLayout(newtab, BoxLayout.PAGE_AXIS));
create JTextPane for display's part of the chat (to have style for conversation like android application such as viber, ....)
I want to be able for following styling:
diffrent alignment
change font, color
insert JComponent (to show other type of messages )
setborder of each message round (I don't want the squre one)
...
context = new StyleContext();
kit = new HTMLEditorKit();
chatPane = new JTextPane();
chatPane.setEditable(false);
chatPane.setContentType("text/html");
chatPane.setEditorKit(kit);
chatPane.setText("");
doc = (HTMLDocument) chatPane.getStyledDocument();
CSS(); // it is for adding ccs style to stylesheet of document
JScrollPane scroll = new JScrollPane(chatPane);
newtab.add(scroll , BorderLayout.CENTER);
My problem is to set perfect stying to my display part, since javax.swing.text.html.CSS provides HTML 3.2 support, so the CSS properties that are supported are limited!
while searching on Internet I find JavaFX, but I don't know is it good to use JavaFX and swing together or even is it possible?!
also which layout manager is better for the JPanel (newtab) to have my JTextPane with scroll.

As its already been said, it is possible to mix Swing and JavaFX especially since Java 8 you can do it both ways:
Embed Swing Components in JavaFX with SwingNode
Embed JavaFX Components in Swing with JFXPanel
Recently we had to make the same decision. We had an application and wanted to migrate to JavaFX to get a more modern design and to make use of all the introduced language features like PropertiesBindings etc., which is nicely supported by JavaFX Components.
So first we tried to embed JavaFX in Swing. All new components were embedded with the help of JFXPanel. It was really easy, but from time to time we had some rendering issues which got more and more annoying. "Unfortunatly" we got used to the new JavaFX API, which is why we deceided redesigning our appliction to make it a JavaFX application with some Swing Parts in it, which was possible, when Java 8 was released, since we didn`t wonna waste time on fixing thoses kind of rendering issues. The redesign was actually some work since some concepts are just different. Benefitting from the new API caused some refactorings, we didnt really wonna do in first place.
But then again mixing Swing and JavaFX got a bit fuzzy, and the look and feel of the application didnt really feel convincing, so then we finally removed all Swing Parts and replaced them by JavaFX Components. So far we don`t regret that step, but it was more work then we expected it to be, eventhough we already used patterns like MVP, where only Views had to be refactored, since presenters were (mostly) free from UI stuff (which was really an interesting process, were we learned a lot about MVP and designing an application).
So in conclusion I just can suggest to create a list of views you have and think of all the components you would need and try to find the corresponding components in JavaFX. Make small examples for the most complex components to see if they fullfill all your usecases. If that is the case and you still have enough time to switch to JavaFX I personally would go for a pure JavaFX approach, because of the experiences I made with mixing JavaFX/Swing, especially since your UI design seems to be in an early state. In the end it is just a question of time you have available for your project and if you are really up to learn about the new concepts and components of JavaFX.
Concerning the JavaFX CSS Support, you find a reference here.

It IS possible to mix JavaFX and Swing. But I have no experience in it. I just did a little FX-UI for a small project which was pretty nice. Especially the CSS-Feature is great.
According to mixing, I just recently found a blog which discouraged mixing both technologies: http://dlemmermann.wordpress.com/2014/07/17/javafx-tip-9-do-not-mix-swing-javafx/
Maybe this gives you a little help.

Recently I was asked same question.
About one month ago I started new project with my team. We use Java 8.0 + JavaFX 2.2.
What problems did I find in JavaFX?
It's new technology, so many issues still not answered. And you must look for it own.
No tray supporting, so you must use java.awt.SystemTray.
Also I found one problem in the design.
For example you want to make beautiful list with cells which contains label which stuck to left side and checkbox about right side. But there is no good way to do it and you have to calculate length of cells and etc..
But JavaFX provide great opportunities for cutomizing GUI. And you can incapsulate your design in jxml file. It's very convient, because it even more separate code from design.
About mixing I think that if platform allows it than you have to use a solution that provided a platform.
And I think that the decision to use JavaFX correct, if only because it is a relatively new technology, developed by Oracle and it probably will soon replace the swing.

Using JavaFX Chart in Swing Application

I have a traditional Java swing application (extends JFrame and has a main class) that uses JFreeCharts for some charting functionality. I have recently seen JavaFX and think these charts look alot refresher and will give my users a better experience. I wish to embed a JavaFX chart scene into a jInternalFrame (which in turn is called from my jDesktopPane).
I have followed a simple tutorial on how to create both a javafx application and a javafx chart but I am stuck on to how I get the scene inside my existing code. One example I have been through shows me how to achieve this but means converting my project to a javafx one which extends "application" class.
How can I achieve what I want? Is it not possible to keep my existing JFrame as the top level class and simply add a JFXPanel to my jinternalframe.
Any help would be great, please note I have been through some tutorials and they require me to convert my project to javafx - I simply want a javafx scene in my existing swing app.
Many thanks,

You don't need to convert your Swing application to a JavaFX application. You can place a JavaFX Chart in a JFXPanel which may be placed in a Swing component. The javadoc I linked includes sample code for embedding a JavaFX node in a Swing application.
Review the official JavaFX for Swing Developers tutorial trail from Oracle.
Also look at the Embedding JavaFX in Swing sample of SwingInterop for embedding a chart in a Swing application. The sample is provided by Oracle under the BSD open source license so that you can use it in your application.
Despite all this, my advice, unless it is a large, existing Swing code base that you just want to use a couple of JavaFX features in, is to write your application as a pure JavaFX application rather than a mixed Swing/JavaFX application.

Is there any JavaFX gui builder?

NetBeans for JavaFX I tried, but its really not stable, lot of things getting often changed and also it does not shift with NetBeans nightly builds. Also I am afraid will JavaFX remain or it will be deprecated by Oracle.
So, I was thinking if there is something else which has more advanced way of doing JavaFX UI designing, as an alternative tools of NetBeans for JavaFX.
Question: Is there any good JavaFX gui builders which generates readable code, with less mess?
Thanks in advance.
ex: http://www.reportmill.com/jfx/

You can try JavaFX Scene Builder to create visualy your FXML files. FXML files are the "UI" of your application! JavaFX Scene Builder is only for JavaFX 2.0!
Here is the documentation: http://docs.oracle.com/javafx/scenebuilder/1/user_guide/jsbpub-user_guide.htm

Swing Menu that can be customized by user

Is there any framework or lib out there to create a Java swing menue that can be edited by the user via drag and drop?
Added: Implementing a polished solution myself can take a lot of time. What i would like to see: display the entry while dragging, opening submenus automaticially, showing a line where the item would be placed when releasing the mouse. Actually like the windows startmenu in XP. This would take a lot of time, i am still hoping to find framework or a subclassed Jmenu with these features.

You can implement drag and drop on most (all?) Swing components. See this tutorial to get started.
Update: based on your updated question. have a look at JFrameBuilder (note that its not free).
JFrameBuilder is an easy-to-use visual Java GUI builder.
JFrameBuilder provides the application GUI solution for Java developers. It enables Java developers to create sophisticated Swing GUI applications using drag-and-drop interface without spending a lot of time writing code.
Personally I find it a lot simpler to write pretty UIs in SWT (the toolkit used by Eclipse), it has more access to the underlying OS and provides a richer experience that's closer to what you're after in my opinion. Here's a guide to implementing drag and drop in SWT.