You can do that with CS3 as well...which is actually what I do. I have the fuselage, wing, horizontal stabilizer, tail, cockpit, and intake and exhaust as separate folders - each with dozens of layers. The fuselage had the most layers and therefore sub-folder within it as well. I don't use masks though. I'm not vey good with them and they don't serve me well. Maybe in After-Effects but not so much in PS. I'm still kind of amateurish with Photoshop so there are many features I still don't understand.