Description of work-in-progress design candidates during the pre-concept and conceptual aircraft design stages have traditionally followed protocol compatible with the later, more mature phases of contemporary product development, i.e. preliminary and detailed design. Up to this moment in time there has been a natural, intuitive tendency to approach design description using geometry as the initial basis upon which all analysis and design refinement could proceed. Design and integration, whether kinematic or structural (static) systems, and irrespective of applications, should be treated as a holistic problem with functionality as opposed to geometric description of a physically tangible artifact being the first step in product definition. This paper presents a coherent, logical method of describing an aircraft concept using functionality as a basis. Hereafter known as Holistic Granular Programming (HGP), any collection of assemblies and components can be described mathematically, and, subsequently analyzed as an engineering safety system. Thereafter, a discussion is given detailing how HGP can be integrated within the Conceptual Design Tool (CDT), an open-source, multi-disciplinary framework for aircraft design currently being developed at Bauhaus Luftfahrt. Independent of any particular tool implementation a number of other questions are addressed, such as: how to map the terminology of HGP onto the concepts used in software engineering, how to model the different aspects of HGP as part of a data meta-model, what necessary steps in a potential HGP workflow can be identified, and, what kind of support can be offered to the designer.