We report results from computational modeling of the relative stability of germanosilicate SCM-15 structure due to different distribution of germanium heteroatoms in the double four-member rings (D4Rs) of the framework and the orientation of the structure directing agent (SDA) molecules in the as-synthesized zeolite. The calculated relative energies of the bare zeolite framework suggest that structures with germanium ions clustered in the same D4Rs, e.g., with large number of Ge–O–Ge contacts, are the most stable. The simulations of various orientations of the SDA in the pores of the germanosilicate zeolite show different stability order—the most stable models are the structures with germanium spread among all D4Rs. Thus, for SCM-15 the stabilization due to the presence of the SDA and their orientation, is thermodynamic factor directing both the formation of specific framework type and Ge distribution in the framework during the synthesis. The relative stability of bare structures with different germanium distribution is of minor importance. This differs from SCM-14 germanosilicate, reported earlier, for which the stability order is preserved in presence of SDA. Thus, even for zeolites with the same chemical composition and SDA, the characteristics of their framework lead to different energetic preference for germanium distribution.