We present an approach to design optimization of multi-cluster embedded systems consisting of time-triggered and event-triggered clusters, interconnected via gateways. In this paper, we address design problems which are characteristic to multi-clusters: partitioning of the system functionality into time-triggered and event-triggered domains, process mapping, and the optimization of parameters corresponding to the communication protocol. We present several heuristics for solving these problems. Our heuristics are able to find schedulable implementations under limited resources, achieving an efficient utilization of the system. The developed algorithms are evaluated using extensive experiments and a real-life example.