My suggestion is to create a new level design program that incorporates tileset design and script design as well. For example if you had JCS, you could supplement the tileset window with a natural tileset drawing or painting tool. That might save you time if your plan is to remake JJ2.

But as for that, my idea is that there are only 3 layers, foreground, middle and background, and within each layer are 3 dimensions, so just place tiles in an order of priority when viewing a busy 3d foreground layer or busy 3d background layer.