I hear what you’re saying. Layers confused the heck out of me for the longest time, then it finally clicked and all started making sense. They are easy to work with now. It would have “clicked” for you too, you just didn’t give it enough time. I love using layers to make collages, especially. I don’t know how one would do it any other way.
Well, I’m sure what I’m actually doing when I do collages and masks is ‘layering’ each object on whatever my background image or canvas is, but somehow, working it all right there on the workspace and moving the active objects forward or back until I merge them feels easy. :)