I suggest you change your workflow to masking layers. I'm not totally sure what you are trying to do, but I think using each color as a layer and then using masks is easier to manipulate than trying to select by color and working in another image.
Here is an example of what I mean:
example.xcf (Size: 9.75 KB / Downloads: 190)
I just changed the color in the top layer...
Here is an example of what I mean:

I just changed the color in the top layer...