Your layers sound seem fine to me, though it's impossible to be more helpful without knowing more about the story. I'm not sure what you're asking about really. If your conflict is interwoven with your setting and it all meshes, go for it and see what happens. Just be wary of spending all your time building the world and skimping on the story and characters. Your goal should be to tell a compelling story about characters with problems who happen to live in this cool world, not a conlfict that only exists to showcase this cool world.
The Layers play only a very small role near the end of the particular story I'm working on at the moment. They're really behind the scenes background at the moment.
To give you some more information, the story takes place in the Kingdoms(which is actually just the closest translation I have right now for a con-word). Sometime in the very distant past, there was something analogous to an ecological succession, but relating to the metaphysical side of the environment. It was the first of three, the other two taking place after the portion of the timeline I'm operating in now. Basically, there are now two sub-Layers in the Kingdoms super-Layer, and the story takes place in the second. Because of the time-scale and inter-connectivity of events, I'll probably forget to mention something. So do ask for clarification if necessary.
Basically, certain groups are trying to reverse the split, or "Derivation". The second phase of this plan is in the works, and it involves the invasion of the northern half of a certain continent, where the protag's home country is located. The invaders are unaware that this is the actual goal of their invasion. For them, it is a religious conflict on an "earthly" scale.
Their God is a remnant of the First Empire, "Empire" being the term for each of the four Kingdoms sub-Layers(sort of... the etymology is backwords(bad pun), here). This God has been recruited just recently by the main orchestrators of this plan. In order to return the world to the it's state prior to the First Derivation, the new "Powers/Spirits"(again, a bad translation), must be sent back to where they came from. In the second stage, this means they must be returned to the Planes. In this part of the world, the first stage has already been mostly completed. Unfortunately, due to unforseen circumstances, the group who perpetrated the first stage are gone. So, during the second invasion, their work is undone. The first section of storyline ends somwhere around there; after that, all "hell" breaks loose, and it gets much too complicated to explain.
Basically, this is not your typical dimension-hopping action story. So, to clarify, my two questions are: "What do people think of this construct? Are there any holes, inconsistencies, possible cliches?" and "Are there any stories already published that are similar--so that I can be aware of what has and hasn't been done, and learn from it?"
Wavy- There are no extraneous lectures in the story, but I as the author am aware of how the system operates, and ths information is available in context to the extent that is necessary.