From a control system perspective, spatially distributed systems offer challenges because of their distributed nature, nonlinearity, and high order. in addition, the control structure for these spatially distributed networks combine discrete and distributed components, in the form of complex arrays of sensors and actuators. Manipulation of the network states may require simultaneous control actions in different parts of the system and may need transients through several operating regimes to achieve the desired operation. A hierarchical, agent-based control structure is presented whereby local control objectives may be changed in order to achieve the global control objective. The performance of the hierarchical agent-based control approach is illustrated in a case study where the interaction front between two competing autocatalytic species is moved from one spatial configuration to another. The multi-agent control system is able to effectively explore the parameter space of the network and intelligently manipulate the network flow rates such that the desired spatial distribution of species is achieved.