I typically create a structure where I have a src/ directory and then other directories exist at the same level. Some of those directories include:
- lib/ - External Libraries
- config/ - Configuration Files
- resources/ - Various resources I use (images, etc)
At that same level, I then create an Ant script to perform my build so that the appropriate config files, resources, lib, etc are copied into my JAR file upon build. It has worked great for me up to this point and is a fairly easy to understand organizational structure.
Update: Accessing my config files is done, typically, by knowing their location and opening them up and reading them in the code. Because I use Ant to build, I make sure that my config files are in a location that I expect. So, for example, in a recent application I created, when I compile, my JAR file is in the top level directory (relative to the application release structure). Then, there is a "main" config file at that same level. And there is a "theme" config file that is in a themes folder.
To read the various files, I just open them up as I would any other file and read them in and go from there. It's nothing particularly fancy but it works well and it makes it easy to manually change configurations if I need to do so.