This is not such an easy question to answer because everyone works differently. How you assemble your layers, and what layers are on top of others depends how the layers are set to react with the ones below them.
First, look here-
http://www.simmerspaintshop.com/foru...ins-voids.html
This gives you some starting basics.
This next tutorial will show you the general mechanics of working with layers-
http://www.simmerspaintshop.com/foru...photoshop.html
But, just about every tutorial below deals with layer set-up in one way or another-
http://www.simmerspaintshop.com/foru...m37-photoshop/
Wolf's suggestion is a good one. If you download a layered template and examine it you'll get a good idea of how the layers are built.
Think of it as building a model, first you need a foundation, the general shapes that the plane is made up of. Then you need the surface details, panel lines, rivets etc. Then you can paint it and add your decals. But where to put the paint and decal layers? See the tutorials
I hope that helps