An Audio Work Unit is not the same thing as the audio file folder. They are not mapped to each other as well. An Audio Work Unit, saved as a .wwu file in the harddrive, stores the structure, including actor-mixers, containers, and various settings of the audio. The original audio file folder, which is an actual folder in your harddrive, stores the source files of the audio files. Whenever you generate soundbanks, the Wwise application convert the audio files and structures to different type of game assets, usually events and compressed audio files, into your game engine.
You can set the default location of your imported audio files in Project > Project Settings > General > Original Audio Files > Folder. But it is still a fixed location. I recommend you just organize the original file folder in a way different from your work units. You will find it very convenient if you name the files properly.