As for organizing sources, I'm a fan of using the maven layout, even if I'm not actually using maven.
Version control is just plain mandatory. Not using version control is like never saving your documents. You should get in the habit of thinking of your filesystem as just a local cache, where you're really saving your files to VC. As preferred version control goes, I would recommend something decentralized like git or mercurial, but even subversion is better than nothing.
I agree with sproingie. Use version control. Even if you just learn the basic code&commit cycle, it will make you less afraid to try new things, and give you the possibility to revert any bad changes. Not to mention that if you use a free service like bitbucket.org, then you get offsite backup for free.
I would fret too much over package layout. Start with the basic layout that sproingie suggested, and put stuff where it seems sensible at the time. If you are using any modern IDE, then you will have built in refactoring tools that will make moving classes to different packages very easy.