Many complex networks are only a part of larger systems, where a number of coexisting topologies interact and depend on each other. We introduce a layered model to facilitate the description and analysis of such systems. As an example of its application, we study the load distribution in three transportation systems, where the lower layer is the physical infrastructure and the upper layer represents the traffic flows. This layered view allows us to capture the fundamental differences between the real load and commonly used load estimators, which explains why these estimators fail to approximate the real load.