Moiré superlattices in twisted van der Waals materials have recently emerged as a promising platform for engineering electronic and optical properties. A major obstacle to fully understanding these systems and harnessing their potential is the limited ability to correlate direct imaging of the moiré structure with optical and electronic properties. Here we develop a secondary electron microscope technique to directly image stacking domains in fully functional van der Waals heterostructure devices. After demonstrating the imaging of AB/BA and ABA/ABC domains in multilayer graphene, we employ this technique to investigate reconstructed moiré patterns in twisted WSe2/WSe2 bilayers and directly correlate the increasing moiré periodicity with the emergence of two distinct exciton species in photoluminescence measurements. These states can be tuned individually through electrostatic gating and feature different valley coherence properties. We attribute our observations to the formation of an array of two intralayer exciton species that reside in alternating locations in the superlattice, and open up new avenues to realize tunable exciton arrays in twisted van der Waals heterostructures, with applications in quantum optoelectronics and explorations of novel many-body systems.