Nanoscale bulk heterojunction (BHJ) systems, consisting of fullerenes dispersed in conjugated polymers as the active component, have been actively studied over the last decades in order to produce high performance organic photovoltaics (OPVs). A significant role in device efficiency is played by the active layer morphology, but despite considerable study, a full understanding of the exact role that morphology plays and therefore a definitive method to produce and control an ideal morphology is lacking. In order to understand the BHJ phase behavior and associated morphology in these devices, we have used neutron reflection, together with grazing incidence X-ray and neutron scattering and X-ray photoelectron spectroscopy (XPS) to determine the morphology of the BHJ active layer in functional devices. We have studied nine model BHJ systems based on mixtures of three poly(3-alkyl thiophenes, P3AT) (A=butyl, hexyl, octyl) blended with three different fullerene derivatives, which provides variations in crystallinity and miscibility within the BHJ composite. In studying properties of functional devices, we show a direct correlation between the observed morphology within the BHJ layer and the device performance metrics, i.e., the short-circuit current (JSC), fill factor (FF), open-circuit voltage (VOC) and overall power conversion efficiency (PCE). Using these model systems, the effect of typical thermal annealing processes on the BHJ morphology through the film thickness as a function of the polythiophene-fullerene mixtures and different electron transport layer interfaces has been determined. It is shown that fullerene enrichment occurs at both the electrode interfaces after annealing. The degree of fullerene enrichment is found to strongly correlate with JSC and to a lesser degree with FF. Based on these findings we demonstrate that by deliberately adding a fullerene layer at the electron transport layer interface, JSC can be increased by up to 20%, resulting in an overall increase in PCE of 5%.