In this paper, a methodology is presented and employed for simulating the Internet of Things (IoT). The requirement for scalability, due to the possibly huge amount of involved sensors and devices, and the heterogeneous scenarios that might occur, impose resorting to sophisticated modeling and simulation techniques. In particular, multi-level simulation is regarded as a main framework that allows simulating large-scale IoT environments while keeping high levels of detail, when it is needed. We consider a use case based on the deployment of smart services in decentralized territories. A two level simulator is employed, which is based on a coarse agent-based, adaptive parallel and distributed simulation approach to model the general life of simulated entities. However, when needed a finer grained simulator (based on OMNeT++) is triggered on a restricted portion of the simulated area, which allows considering all issues concerned with wireless communications. Based on this use case, it is confirmed that the ad-hoc wireless networking technologies do represent a principle tool to deploy smart services over decentralized countrysides. Moreover, the performance evaluation confirms the viability of utilizing multi-level simulation for simulating large scale IoT environments.