With the default settings, you will have a separate folder for each project you create and the audio folder for that project will be a subdirectory. This is useful if you want to play with those audio (wav) files in another editor or such, since you can find them.
Edit: The "bundle" option will embed all of the files for the project into a single file, which is useful for sending "everything" to someone else, but is not preferred for projects you work with on your machine.