Precise control of the complex morphology of organic photovoltaic bulk heterojunction (BHJ) active layers remains an important yet challenging approach for improving power conversion efficiency. Of particular interest are the interfacial regions between electron donor and acceptor molecules where charge separation and charge recombination occur. Often, these interfaces feature a molecularly mixed donor-acceptor phase. This mixed phase has been extensively studied in polymer:fullerene systems but is poorly understood in state-of-the-art polymer:non-fullerene acceptor blends. Accurate, quantitative characterization of this mixed phase is critical to unraveling its importance for charge separation and recombination processes within the BHJ. Here, we detail X-ray and neutron scattering characterization techniques and analysis methods to quantify the mixed phase within BHJ active layers. We then review the existing literature where these techniques have been successfully used on several different material systems and correlated to device performance. Finally, future challenges for characterizing non-fullerene acceptor systems are addressed, and emerging strategies are discussed.