This conversation has been merged. Please reference the main conversation: Photoshop: Transparency in gradient maps.
As a basic test, create the following layers, top to bottom:
1. Gradient Map
2. White with black squiggles
Set the gradient map so that it runs from 100% opaque red to 0% opaque red.
What I see: the entire picture goes red
What I want to see: the squiggles go red, the white shows through.