This paper reviews the challenges and research gaps in calculating reference points from spatially-structured stock assessment models used within current fisheries management systems. We discuss methods for US and international fisheries that calculate equilibrium values and associated management quantities for fishery populations with spatial structure. Such fisheries inherently violate the assumption of a single well-mixed stock. Accounting for spatial structure accurately and easily is a major goal for the next generation of stock assessment software development. We propose a new method for calculating equilibrium quantities within a spatially- structured model and compare it to a widely-used method (Stock Synthesis) for a set of scenarios. The proposed method aims to reconcile localized recruitment dynamics, which have previously hindered the calculation of equilibrium quantities for fishery populations structured as such. Our results show that the proposed method can respond more precisely to local population dynamics by unmasking localized depletion, a known problem in global-recruitment approaches. Finally, we address areas of research and development needed to integrate spatial models within existing management systems.