Great that you found such a useful use of Stereo Tool!
To store the output on disk, in Winamp, go to Options -> Preferences -> Plug-ins -> Output. Then select Nullsoft Disk Writer (out_disk.dll). (I think it's included in the standard Winamp installation, if not you can download it from the Winamp site).
Note that this will give you a .WAV file. If you want another format, like MP3, Ogg etc., go to http://www.winamp.com/plugins/browse/7
. (For MP3, use for example http://www.winamp.com/plugins/details/143606