The problem that this paper investigates, namely, optimization of overlay computing systems, follows naturally from growing need for effective processing and consequently, fast development of various distributed systems. We consider an overlay-based computing system, i.e., a virtual computing system is deployed on the top of an existing physical network (e.g., Internet) providing connectivity between computing nodes. The main motivation behind the overlay concept is simple provision of network functionalities (e.g., diversity, flexibility, manageability) in a relatively cost-effective way as well as regardless of physical and logical structure of underlying networks. The workflow of tasks processed in the computing system assumes that there are many sources of input data and many destinations of output data, i.e., many-to-many transmissions are used in the system. The addressed optimization problem is formulatedin the form of an ILP (Integer Linear Programing) model. Since the model is computationally demanding and NP-complete, besides the branch-and-bound algorithm included in the CPLEX solver, we propose additional cut inequalities. Moreover, we present and test two effective heuristic algorithms: tabu search and greedy. Both methods yield satisfactory results close to optimal.