I have figured out what was wrong with the smoke, I could render it but I could not see it but it was there just the same, thank you. Now when I try and render two different smoke colors they both come out the same. I have gone into the compositor and created two different settings but I cannot apply them, also when creating two separate domain boxes and two emitters they only take one setting. I have tried to put them on separate layers but this does not work either, I do not want to go into the video sequence editor as this is long. Is there a solution for this?
It sounds like your materials or your textures or your caches are linked. You can check this by changing one setting for Smoke A and see if it applies for Smoke B. If so, then your issue is linking.
To get rid of the link, click the button with the number on it next to the material and texture. That should fix it.