The development of useful structure-function relationships for materials that exhibit correlated nanoscale disorder requires adequately large atomistic models which today are obtained mainly via theoretical simulations. Here, we exploit our recent advances in structure-refinement methodology to demonstrate how such models can be derived directly from simultaneous fitting of 3D diffuse- and total-scattering data, and we use this approach to elucidate the complex nanoscale atomic correlations in the classical relaxor ferroelectric PbMg1/3Nb2/3O3 (PMN). Our results uncover details of ordering of Mg and Nb and reveal a hierarchical structure of polar nanoregions associated with the Pb and Nb displacements. The magnitudes of these displacements and their alignment vary smoothly across the nanoregion boundaries. No spatial correlations were found between the chemical ordering and the polar nanoregions. This work highlights a broadly applicable nanoscale structure-refinement method and provides insights into the structure of PMN that require rethinking its existing contentious models.