Motivated primarily by the problem of UAV coordination, in this paper we address the problem of coordination of a non-homogeneous group of non-holonomic agents with input constraints. In the first part of the paper, we develop a modeling framework for heterogeneous multi-agent systems that is based on timed automata. To this extent, an appropriate abstraction of the agents' workspace from our previous works is extended to three-dimensional space, by utilizing hexagonal prisms. The low level agent details are abstracted by virtue of appropriate controllers to motion primitives that can be performed in the individual workspace cells. The resulting models of the non-homogeneous system capture the non-holonomic behavior and the input constraints imposed by the considered systems. In the second part of this paper, we use the developed models in conjunction with formal verification tools to verify the safety and liveness properties of the system, captured by Linear Temporal Logic (LTL) specifications. Using counter-example guided search, we obtain trajectories that satisfy spatio-temporal specifications. Finally, we simulate two case-studies for two and three-dimensional workspaces respectively.