In FBX SDK, a mesh can have multiple layers. A layer (class KFbxLayer) is a container for a layer element (class KFbxLayerElement) that will affect how the mesh will be rendered.
Unless you need more than one layer (for some advanced purpose), always use layer 0 and only layer 0. MotionBuilder, FBX for QuickTime, and the FBX plug-ins for 3ds Max and Maya only process normals and materials stored in layer 0.