screw photoshop and screw gimp. get Paint.NET. It's WAY better than photoshop, it's free, and has native support for DDS and TGA, no plugins required.
either way, in any program, making a transparent part of texture is just using the eraser in those areas. then once you are converting the textures in assman, in the framebuffer operations section, you need to set the polygon offset to "static decal" and set the alphaTest as "GE128".

just in case I wasn't clear enough. I tend to be horrible at explaining things.