You won't be able to. You can add 3D geometries to the file, and where both exist, you will be able to toolpath both together, but you won't be able to merge more data in to the STL. That's just the way it is with STLs. You could modify the STL in different software, like Blender, Sculptris, etc (may need to convert to OBJ first, which you can do in MeshLab). STL is really point cloud data, not a 3D model of the same form as most CAD programs use.