I just discovered a method to control Filter output location:
a) define 1 Temporary track covering the entire audio file
Set the 1 Temporary track name to be the output file name you want.
c) make this Temporary track the ONLY Active track (uncheck any other tracks in the Track window)
d) Use File>Save Active Tracks and Select "Apply filters" check box
Note: any other tracks definitions will be lost in the filtered file.
Spin Doctor then presents a dialog to select the location for the output file. Chose a folder on a hard drive different from the current (input) audio file. Output file has the Temporary Track name you specified.
Then, on the filtered file you can define the real tracks that will be used to pass to Toast or iTunes.
Any other suggestions for accomplishing this?