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Layers basically means their made up of a bunch of other pieces.
Using the same layers though a player can take each part of his ship and assign one of two things to it, a colour or a small graphic texture round about the size of a banner. The texture would obviously have to tile well if you applied it to a section of the ship. As for colouring sections, you merely set the RBG value of the ship section. Since the game runs with a 3d engine in a 3d enviroment shading of the ship is applied by the engine's lighting, so a basic colour would be shaded, a texture would get added depth etc. With this system there's no pesky out of game downloads and no more downloading then SubSpace banenrs really.