The efficiency of organic solar cells can be increased by careful control of the nanoscale morphology of a dispersed bulk heterojunction device. Atomic force microscopy (AFM) has often been used to characterize morphology but debate persists over the value of traditional AFM measurements since the technique only addresses the active layer topography, and provides insufficient contrast to differentiate between components in a well-mixed composite. Using newer Kelvin Probe Force Microscopy (KPFM) and Quantitative Nanomechanical Mapping (QNM) modes, we demonstrate contrast due to differing elastic modulus and surface potentials between donor and acceptor materials and highlight the value of these techniques to understand critical materials properties as part of a comprehensive nanomorphology study. We test the value of our approach using blends of each of two anilinic squaraines with phenyl-C61-butyric acid methylester. These two squaraine materials differ in chemical compatibility with the standard fullerene acceptor. We vary annealing conditions for our blended films and use the described AFM approaches to demonstrate changing domain sizes, which are affected by chemical compatibility with the fullerene. We demonstrate how KPFM measurements go beyond QNM to provide contrast between materials with reproducibility at a higher image resolution. With the ability to measure contrast between donor and acceptor material, we make a strong case for non-destructive microscopy data to measure effects of variations in annealing temperature on squaraine film morphology, which we confirm influences device performance and efficiency. These conclusions are important for informing material selection for long-term use of associated commercial devices in the field.