Hi guys,
Newbie in need of help

I have been trying to retexture a model to create a clone with different paintjob. Having some problems though, so I thought to ask you for guidance.
When I load .dds file in Gimp it looks like this:
I then make a new layer, insert and edit new textures there. When I'm ready I merge the new layer with the old one and export as .dds.
Thing is, the changed bits lack something. They are not... how to say it - "partially transparent" like the original textures (no checkerboard all over them). Upon loading in game,they have a problem with lighting: when direct sunlight is reflected by the surface it becomes almost white, looking like some extremely reflective polished metal. This would be perfect if I was making a sci-fi starfighter but looks out of place on worn-down Messerschmitt.
Obviously I am missing something, so how to do it correctly?