Which is the correct way to program a Desktop Application???

Hello all,
I haven't programmed in a while and I just got the free Netbeans 6.1 CD just for kicks and to try it out. I'm making a basic application for a store that one of my family members has. I was programming away as I could and right now I came to a conclusion... I think I maybe doing this wrong.
I have done all the GUI using the Netbeans IDE plugin visual designer and I just click on the button and add the event and then I program away. But just right now I noticed another file that is called NameOfProgramApp.java. Then I look to the right and I have NameOfProgramView.java where I have been placing most of my code. Is this the right place to put the code???
I think I maybe missing something or maybe doing some lousy code writing. Any help would be awsome. Is this where I put my Object Oriented think hat on to accomplish the correct way??
Thanks in advance and it feels good to be back :D

A general rule of thumb that I use it to think in layers...
--GUI {What you show the use}
--GUI code logic {local rules and edits}
--WEB/Network {interface for multiuser}
--BUSINESS RULES {rules and coding to make your business work}
--DATABASE {where do you store your durable data}
Granted, this is a very simplistic look, but it will get you a start a thinking process for your app.

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