I'm not clear what you are asking, but I suspect that yes, there is a way to do what you are looking for using layer masks. Perhaps you are having problems from having too many stacked layer masks, so that the lower ones are never visible? If so, I'd advise you to start at the bottom with the base terrain and use succeeding layer masks to build up the terrain from a base of white/invisible, darkening as needed.

In any case, you should check out JFrazier's tutorial on using layer masks in Gimp '[Award Winner] Explanation of Layer Masks in GIMP(and PS)' - even if it does not answer your question it should give you enough information to ask it! http://www.cartographersguild.com/tu...s-gimp-ps.html