You're welcome.
As you can see from the image I'm using Eclipse and I just drag and drop files into the package view wherever I want them.
You're probably right: get some more straight forward experience under your belt - of both Java and Eclipse - and then come back to the problem. Somewhere above I linked to the section in Oracle's Tutorial about creating jar files. It takes more work this way but I have found that what they say there, and in general being able to build simple applications from the command line, really helps when it comes to understanding all the options presented to you by an IDE like Eclipse.