Hexagonal boron nitride (hBN) is a promising host material for room-temperature, tunable solid-state quantum emitters. A key technological challenge is deterministic and scalable spatial emitter localization, both laterally and vertically, while maintaining the full advantages of the 2D nature of the material. Here, we demonstrate emitter localization in hBN in all three dimensions via a monolayer (ML) engineering approach. We establish pretreatment processes for hBN MLs to either fully suppress or activate emission, thereby enabling such differently treated MLs to be used as select building blocks to achieve vertical (z) emitter localization at the atomic layer level. We show that emitter bleaching of ML hBN can be suppressed by sandwiching between two protecting hBN MLs, and that such thin stacks retain opportunities for external control of emission. We exploit this to achieve lateral (x-y) emitter localization via the addition of a patterned graphene mask that quenches fluorescence. Such complete emitter site localization is highly versatile, compatible with planar, scalable processing, allowing tailored approaches to addressable emitter array designs for advanced characterization, monolithic device integration, and photonic circuits.