We consider the optimal control problem of steering a collection of agents over a network. The group behavior of an ensemble is often modeled by a distribution, and thus the optimal control problem we study can be cast as a distribution steering problem. While most existing works for steering distributions require the agents in the ensemble to be indistinguishable, we consider the setting where agents have specified origin-destination constraints. This control problem also resembles a minimum cost network flow problem with a massive number of commodities. We propose a novel optimal transport based framework for this problem and derive an efficient algorithm for solving it. This framework extends multi-marginal optimal transport theory to settings with capacity and origin-destination constraints. The proposed method is illustrated on a numerical simulation for traffic planning.