There are many many different paths you can take. I like to (generally, if I can) keep geographic regions together in my layers list, so that if I change one part of the upper left wing, for example, all the other parts are readily accessible and can be updated to reflect this change.
The complex interaction of layers means that you may want to do something with where panel lines and rivets are on top of markings but below the weathering. If you separate parts (wings, fuselage, etc) like I try to, then you sometimes run into problem where putting the panel lines and rivets at layer #10 works just fine for the wing, but the fuselage layers start at #20, and now is below them....
So the end result is I try to make my markings and my details, and all that in layer groupings. Then I try to put the overall panel lines and rivets above them all. This way (generally speaking) works pretty well.
If I need to move my panel lines down to be between specific layers, I will often do the following: Put the panel lines/rivets on top of everything, get all the settings/blendings correct, then create a layer mask that eliminates all pixes around the area in question -- let's use the wing example. So now I have panel lines on all parts except that wing. The pixels are still there, they are just masked. I copy the layer, and move the copy down to the layer hierarchy where I need it. Then I just invert the mask. Now I have 2 identical layers, only they show up in mutually exclusive spots. If I make any changes to the blending of the "top" panel lines layer, I know I also duplicate these changes to the "wing" layer.
If you see what I mean. That's much less common but I have done some things like that on a number of skins.