The manipulation of a collection of fluid particles in a low Reynolds number environment has several important applications. As we demonstrate in this paper, this manipulation problem is related to the scientific question of how fluid flow structures direct Lagrangian transport. We investigate this problem of directing the transport by manipulating the flow, specifically in the Stokes flow context, by controlling the strengths of two rotors fixed in space. We demonstrate a novel dynamical systems approach for this problem and apply this method to several scenarios of Stokes flow in unbounded and bounded domains. Furthermore, we show that the time-varying flow field produced by the optimal control can be understood in terms of dynamical structures such as coherent sets that define Lagrangian transport. We model the time evolution of the fluid particle density using finite-dimensional approximations of the Liouville operators for the microrotor flow fields. Using these operators, the particle transport problem is framed as an optimal control problem, which we solve numerically. This framework is then applied to the problem of transporting a blob of fluid particles in domains with different boundary conditions: free space, near to a plane wall, in a circular confinement, and the transport of two distributions of particles to a common target. These examples demonstrate the effectiveness of the proposed framework and also shed light on the effects of boundaries on the ability to achieve a desired fluid transport using a rotor-driven flow.