This paper presents a methodology for simulating the Internet of Things (IoT) using multi-level simulation models. With respect to conventional simulators, this approach allows us to tune the level of detail of different parts of the model without compromising the scalability of the simulation. As a use case, we have developed a two-level simulator to study the deployment of smart services over rural territories. The higher level is base on a coarse grained, agent-based adaptive parallel and distributed simulator. When needed, this simulator spawns OMNeT++ model instances to evaluate in more detail the issues concerned with wireless communications in restricted areas of the simulated world. The performance evaluation confirms the viability of multi-level simulations for IoT environments.