Deep Paint treats anything imported from Photoshop as a single image, ad disregards layers. When exported back to Photoshop, the layer will be correct, but it doesn't help if you need the stuff below your layer for a guide when painting in Deep Paint. What I do is copy the image and send the copy to Deep Paint, then I put the newly deep painted image on top of my existing image as a new layer. It's a pain in the butt to take the extra steps, but it works.