We consider the issue of synthesis and analysis of multidimensional controlled model with consideration of predator-prey interaction and taking into account migration flows, and propose new formulations of corresponding optimal control problems. In search for optimal trajectories, we develop a generalized algorithm of global parametric optimization, which is based on the development of algorithm for generating control function and on modifications of classical numerical methods for solving differential equations. We present the results of the search for optimal trajectories and control functions generation. Additionally, we propose an algorithm for the transition to stochastic controlled models based on the development of a method for constructing self-consistent stochastic models. The tool software as a part of a software package for modeling controlled dynamical systems has been developed. We have also carried out a computer study of the constructed models. The results can be used in the problems of modeling dynamics processes, taking into account the requirements of control and optimization.