I don't recommend using an IDE to generate your code. You spend time learning the IDE and not learning Swing.
The key to layout design is to logically group components onto a panel and then use an appropriate layout manager to display the components.
The trick is that you can nest panels with different layout managers as necessary.
Maybe start with the working code found in the Swing tutorial on How to Use Lists
The tutorial also has a section on "Layout Manager" which contains working examples of each layout manager on its own.
I'm not sure why you show the bottom row with 3 columns, since there are no components being displayed.
So assuming you really only need a layout with 3 columns I might suggest you start with:
1. use the default BorderLayout of the frame
2. Add your JScrollPane containing the JList to the BorderLayout.LINE_START
3. Create a JPanel with a GridLayout and add it to the BorderLayout.CENTER
4. Create a panel for the "Add From File" components and add components to the panel and add the panel to the grid layout panel
5. Create another panel for the "Class Name" components and add the panel to the grid layout panel
so the key to to start with a top level logical design for each panel and then repeat the process as you get into more detail for each panel.
You will eventually learn which layout manager to use in a particular situation.