This paper suggests a control method for an efficient topology/parameter evolution in a bond graph-based GP design framework that automatically synthesizes designs for multi-domain, lumped parameter dynamic systems. We adopt a hierarchical breeding control mechanism with fitness-level-dependent differences to obtain better balancing of topology/parameter search - biased toward topological changes at low fitness levels, and toward parameter changes at high fitness levels. As a testbed for this approach in bond graph synthesis, an eigenvalue assignment problem, which is to find bond graph models exhibiting minimal distance errors from target sets of eigenvalues, was tested and showed improved performance for various sets of eigenvalues.