I assume "a" and "e" refer to axial and equatorial groups.
Your initial idea of comparing the energies of the various ring flipped conformations of the two compounds should give you a good idea. The major interactions to look at are the 1,3-diaxial interactions and the 1,2-gauche interactions.
My off-the-cuff calculations for 1,2-dimethyl cyclohexane suggest an energy difference of about 1.8 kcal/mol between the most stable conformations of the cis and trans isomers (trans being more stable).