What I have done when confronted with such a problem, and I don't have the native files, what I have done I take an image of the upper layer and color it red, the bottom layer, color it green, and the silkscreen color it black.
I then open up all images in Photoshop or Gimp, and attach them as, well, layers.
Both programs allow you to control the transparency of each layer and thus is fairly straightforward to follow the traces in a two layer board.