Well, I assume from your question that you don't know a lot about version control, so I'll give you a brief intro. To have effective version control, you'll have to have a version control system (like CVS, subversion, MS visual source safe, Mercurial, etc). Those systems/servers contain repositories for the files you need to have under version control. Every time you change a file on your system, you can commit it to the repository, and it saves the changes. You can go back to any previous version. You can have many branches, and integrate them later, and many other features. You do not have to store new versions in different locations. The version control system manages everything for you.
Now, what does netbeans have to do with that? Well, netbeans comes with default support for CVS and subversion (and Mercurial in version 6.1). This means that you can put the whole project in one of those version control systems, and you can update from and commit to the repository from within netbeans itself. You can also view differences and history from netbeans, which is great. All you'll need to do is have your version control system installed and configured on the server you want, and you'll be connecting to it using netbeans.