The innovative concept of Electric Aircraft is a challenging topic involving different control objectives. For instance, it becomes possible to reduce the size and the weight of the generator by using the battery as an auxiliary generator in some operation phases. However, control strategies with different objectives can be conflicting and they can produce undesirable effects, even instability. For this reason an integrated design approach is needed, where stability can be guaranteed in any configuration. In other words, the design of the supervisory controller must be interlaced with that of low-level controllers. Moreover, uncertainties and noisy signals require robust control techniques and the use of adaptiveness in the control algorithm. In this paper, an aeronautic application aiming at recharging batteries and to use the battery to withstand generator overloads is addressed. Detailed and rigorous stability proofs are given for any control configuration, including the switching phases among different control objectives. Effectiveness of the proposed strategies is shown by using a detailed simulator including switching electronic components.