This paper addresses the problem of coordinating dynamical systems with possibly different dynamics (e.g., linear and nonlinear, different orders, constraints, etc.) to achieve some desired collective behavior under the constraints and capabilities of each system. To this end, we develop a new methodology based on reference conditioning techniques using geometric set invariance and sliding mode control: the sliding mode reference coordination (SMRCoord). The main idea is to coordinate the systems references. Starting from a general framework, we propose two approaches: a local one through direct interactions between the different systems by sharing and conditioning their own references and a global centralized one, where a central node makes decisions using information coming from the systems references. In particular, in this work we focus in implementation on multivariable systems like unmanned aerial vehicles (UAVs) and robustness to external perturbations. To show the applicability of the approach, the problem of coordinating UAVs with input constraints is addressed as a particular case of multivariable reference coordination with both global and local configuration.