The past decade has seen an explosion in the availability of spatial data, not only for researchers, but the public as well. As the quantity of data increases, the ability to effectively navigate and understand the data becomes more challenging. Here we detail a conceptual model for a spatially explicit database management system that addresses the issues raised with the growing data management problem. We demonstrate utility with a case study in disease ecology: to develop a multiscale predictive model of African trypanosomiasis in Kenya. International collaborations and varying technical expertise necessitate a modular open-source software solution. Finally, we address three recurring problems with data management: scalability, reliability, and security.