This script will place your Render Element files in named subfolders according to where the main pass is stored and what the name of the Render Element is.
Example:
Main pass is set to render to:
C:\myProject\renderoutput
Rendered Elements like Alpha, Specular, Diffuse etc. will be placed at:
C:\myProject\renderoutput\Alpha
C:\myProject\renderoutput\Specular
C:\myProject\renderoutput\Diffuse
etc.
Enable this script as a Pre-Render script:
Render Setup Dialog -> Common Tab -> Scripts -> Pre-Render -> browse for the script file