The statistics of vertical structure of the turbulence affect the complexity of the design and implementation of Multi-Conjugate Adaptive Optics (MCAO) systems. The operation of these systems could be optimized if the stability of the layers were such as to permit to fix the deformable mirrors (DMs) at specific heights. Moreover, it is desirable to know the effects on the placement of the DMs and the gain of the isoplanatic angle in terms of site characterization. From the turbulence profiles measured with the G-SCIDAR technique we have analyzed the statistics of the heights of the DMs and the resulting isoplanatic angles. These results are based on the data from a long ongoing campaign at Roque de los Muchachos Observatory (La Palma) and Teide Observatory (Tenerife) with the highest statistical coverage to date. We have used two ideal MCAO systems, consisting of two and three DMs, and, from a specific comparison in simultaneous measurements over two nights, we show the evolution of the position of DMs and isoplanatic angles in both sites, which can sporadically reach values greater than 60" in 500 nm. We also study the effects of the stability of the conjugate planes on the improvements in the isoplanatic angles.