I'm not going to say I know the proper way, but what I usually do is this:

1. Open a texture in DXTBmp and send it to my editor, Paint Shop Pro.

2. Create a new layer.

3. Duplicate all the lines, rivets, etc on the new layer, including any text so I will know the orientation of it when I do a repaint.
Another way to do this is to create a duplicate layer, select all the colored areas between the lines, and erase/delete.

4. Change to the base layer and use the magic wand to select all the areas in between the parts, then invert the selection.

5. Lighten the selection until all color is gone. Save as a .psd with layers intact in a new folder titled paint kit in the particular aircraft main folder.

6. When I get ready to do a repaint, I open the file and create my new paint, then save to a new folder in my Repaint folder, but don't save the original that is going back into the paint kit folder.

7. When I get to the point of wanting to check my work, I then open the first texture of an existing paint in DXTBmp and send the alpha to the editor.

8. Make a duplicate of the alpha and close the original.

9. Then open the same texture that I have been working on in DXTBmp and send the alpha to the editor.

10. Copy the one I duplicated and paste it into the one I just sent to the editor. Close it and save.

11. Then save the new texture to a new texture folder in the Aircraft folder, saving as the same (DXT5, etc) type as the original.

Now if I need to work on it some more. I open the .psd in my repaint folder in my paint program, not the one in the texture folder. When finished, I repeat the above procedure (numbers 7-11) for the alpha channel and save as DXT to the aircraft folder.

Hope this helps.