Scanning tunneling microscopy was used to study the effect of the electron-accepting unit and the alkyl substituent's position on the type and extent of 2D supramolecular organization of penta-ring donor-acceptor-donor (DAD) semiconductors, consisting of either tetrazine or thiadiazole central acceptor ring symmetrically attached to two bithienyl groups. Microscopic observations of monomolecular layers on HOPG of four alkyl derivatives of the studied adsorbates indicate significant differences in their 2D organizations. Ordered monolayers of thiadiazole derivatives are relatively loose and, independent of the position of alkyl substituents, characterized by large intermolecular separation of acceptor units in the adjacent molecules located in the face-to-face configuration. The 2D supramolecular architecture in both derivatives of thiadiazole is very sensitive to the alkyl substituent's position. Significantly different behavior is observed for derivatives of tetrazine (which is a stronger electron acceptor). Stronger intermolecular DA interactions in these adsorbates generate an intermolecular shift in the monolayer, which is a dominant factor determining the 2D structural organization. As a consequence of this molecular arrangement, tetrazine groups (A segments) face thiophene rings (D segments) of the neighboring molecules. Monolayers of tetrazine derivatives are therefore much more densely packed and characterized by similar π-stacking of molecules independently of the position of alkyl substituents. Moreover, a comparative study of 3D supramolecular organization, deduced from the X-ray diffraction patterns, is also presented clearly confirming the polymorphism of the studied adsorbates.