We outline a step-by-step protocol that incorporates a number of theoretical and computational methodologies to evaluate the structural and electronic properties of π-conjugated semiconducting materials in the condensed phase. Our focus is on methodologies appropriate for the characterization, at the molecular level, of the morphology in blend systems consisting of an electron donor and electron acceptor, of importance for understanding the performance properties of bulk-heterojunction organic solar cells. The protocol is formulated as an introductory manual for investigators who aim to study the bulk-heterojunction morphology in molecular details, thereby facilitating the development of structure-morphology-property relationships when used in tandem with experimental results.