Despite their widespread use, the mechanisms governing the synthesis of zeolite catalysts are still poorly understood. A notable example of this problem is the uncertainty surrounding the influence of synthesis conditions on the placement of Al atoms in the zeolite framework, which determines the active sites available for catalytic species. In this work, the role of the cis to trans isomer ratio of the OSDA N,N-dimethyl-3-5-dimethylpiperidinium on the energetics of 26 distinct Al pair distributions in SSZ-39 is examined both in the presence and absence of Na using density functional theory calculations. The initial orientation of the OSDA was found to have a significant impact on the final energies present, necessitating the screening of a large number of initial orientations with force field calculations and single point DFT calculations. Ground state energies were found to vary significantly with the ratio of cis to trans OSDAs with a Boltzmann distribution revealing the most likely Al pair distributions shift from sharing the same 8 membered rings to sharing the same double 6-membered rings to having no shared subunits as one increases the amount of cis OSDA present within the framework. The presence of Na was found to favor Al pair distributions where both Als occupied the same 6-membered ring. When an implicit solvent model was used to evaluate ground state energies the ideal Na sites shifted from 6membered rings to empty SSZ-39 cages while OSDA positions and orientations remained largely the same. To provide insight on how kinetic factors may influence Al distributions, formation energies we calculated for connected double 6-membered rings. These formation energies revealed a preference for Al pairs to occupy the same 4-membered ring, which indicates kinetic and thermodynamic control may lead to different Al distributions in SSZ-39.