Well one way I've found once I've added so many layers of color and other stuff, just grab all those layers (that involved my forests etc) copied it to another image, flattened them together and pasted it back in, there might be a bit of a difference depending on the transparency levels and blend modes, but in general I can usually get the entire group of layers to match up in the one, so then I can do as Ascension purposed, making that cloud layer and putting it over the top.... I haven't read through your tutorial, but just a thought, and maybe you've already done this but hey thought I'd pass it along...

oh and always keep the originals of those layers, as you probably already know about =P