The adequate allocation of human resources is one of the most important success factors in software projects. Although project teams can be regarded as complex systems in which a team’s performance is highly influenced by the interdependencies among team members, the allocation methods applied to date have focused only on individual skills and consider project teams as units of isolated workers. The existing software project scheduling problem (SPSP) is extended to (1) consider different skills and efficiencies of employees and (2) examine the pairwise synergies between them, as well as to (3) handle the flexible structure of the project that is used in flexible management, such as agile project management. To better understand the impact of synergies on the project’s cost, the solutions of the traditional and extended SPSP versions are analyzed and compared on the generated project networks. The results show not only that this factor has a highly significant impact but also that the project cost strongly depends on the structural parameters of the synergy network (e.g., topology, network size and degree centrality). Among these parameters, a low degree of centrality and some topologies, most notably star and circular networks, obtained the highest reduction in the projects’ total cost.