NetBeans has its own directory structure that is not the same as the one unzipped I'm not sure I understand this. Does NetBeans really force you to layout your software projects the way it wants? If that's the case nobody would ever use it on software started using some other method, and tht's nuts!
Are you really sure that NetBeans doesn't have a way to create a new project from your existing source code?
A quick look round the web led me to
http://java.sun.com/developer/onlineTraining/tools/netbeans_part1/ which states:
Importing Existing Java Source Code Into NetBeans
You can use two project templates to import your existing source code:
Java Project With Existing Sources -- Use this project template to create a standard Java project. A standard Java project uses the IDE to compile, run, and debug your application.Java Project With Existing Ant Script -- Use this project template to create a free-form Java project. A free-form Java project uses your own Ant script to compile, run, and debug your project.
The following steps cover use of the first template to create a standard Java project without the use of existing Ant scripts.
Choose File -> New Project (Ctrl-Shift-N).Choose General -> Java Project With Existing Sources.Click Next.In the Project Name field, type a name for your project. Notice that the IDE automatically suggests a name for the project folder.Click the Browse button next to the Project Folder field and create a folder somewhere on your system for your NetBeans projects. Then select the newly created NetBeans projects folder. Be sure to select the Set as Main Project box, then click Next.In the Source Packages Folder pane, click Add Folder, navigate to the directory of source files, and select the resources and src folders.(Optional) In the Test Packages Folder pane, click Browse to select the folder containing the JUnit package folders.Click Finish.
Your project will now be displayed in the Projects and Files windows.
Does that help?