Multi-conjugate adaptive optics (MCAO) uses two or more deformable mirrors (DMs) at conjugate altitudes approximately matched to the atmospheric turbulence layers to increase the corrected field of view. An important unresolved problem for MCAO is determining the optimal sequence of the DMs. Theoretical considerations and numerical studies suggest that ordering the DMs from lowest to highest altitude reduces the effects of scintillation, whereas on-sky experiments report that the best performance is attained with the ground-layer DM placed last. Using analytical calculations and numerical experiments with Fresnel propagation of Kolmogorov turbulence, we demonstrate that the scintillation results from spatial frequencies higher than the spatial sampling of high-altitude DMs are able to correct. Hence, the effect of scintillation is not impacted by MCAO correction regardless of the sequence of the DMs. Using end-to-end numerical simulations, we find that the dynamic misregistration between the DMs and the wavefront sensors is minimized by placing the ground-layer DM last, leading to increased loop stability and lower wavefront errors. Contrary to conventional wisdom, we recommend that the DMs be sequenced from highest to lowest altitude.