v1.83:
Settings, General Settings, Naming tab:
Check: Use sub directories only for mp3 and wma
This doesnt seem to be configurable re: actual folder for WAV files, but it will store them at the same directory level as the Sub Directories specified just above that parameter (instead of where the MP3 files are stored).
Also, specify a Directory to store files in: i.e. C:\Ripped_music
It will store the WAV files there, with the MP3 files in the Artist/Album Sub Directories specified in the associated check-boxes.
This may not be optimal, but will indeed separate the WAVs from the MP3s.