Ternary spinel oxides are actively used and researched for applications ranging from electronics, sensors, catalysis, data storage, to energy storage due to their useful magnetic, catalytic, and electronic properties. One intriguing nanomaterial is the non-stoichiometric p-type spinel CoxMn3-xO4, in which cation site occupation is an important determinant of materials properties. Therefore, by manipulation of cation configurational disorder, properties such as the charge carrier density and the associated electrical conductivity can be easily controlled. The manipulation of cation configuration disorder is carried out by changing the Co to Mn ratio (or the ‘x’ value in CoxMn3-xO4), which leads to the variation of (1) atomic distribution of Co and Mn atoms present at tetrahedral (Td) and octahedral (Oh) sites in the spinel system, and (2) oxidation states of the cations. In this work, we utilize a new technique to characterize the configurational disorder in spinels. We demonstrate that x-ray emission spectroscopy (XES) is a more reliable method than traditionally used K-edge x-ray absorption spectroscopy (XAS) to extract cation site occupation. Comparison between the XAS and XES techniques reveal that XES provides not only the site occupation information that XAS reports, but also additional information on the valence states of the cations at each site. We show that the XES error is lower than the EXAFS error in all cases, by up to ~20%. Additionally, the error for EXAFS is as high as 35% whereas for XES, the error determined is consistently smaller than 10%. Furthermore, we correlate the extracted site occupation data to the electrical conductivity and the supercapacitor performance and observe a strong correlation between structural properties and electronic properties of spinels. We show that the number of hole acceptor/donor pairs of Mn2+/Mn3+ at Oh sites is proportional to both the electrical properties and the energy density of the supercapacitors. Finally, via the optimization of configurational order in the CoxMn3-xO4 nanoparticles system, we were able to increase the energy density and specific capacitance of the supercapacitors by 2x as compared to previously reported values.