The joint optimization of physical parameters and controllers in robotic systems is challenging. This is due to the difficulties of predicting the effect that changes in physical parameters have on final performances. At the same time, physical and morphological modifications can improve robot capabilities, perhaps completely unlocking new skills and tasks. We present a novel approach to co-optimize the physical layout and the control of a cooperative aerial transportation system. The goal is to achieve the most precise and robust flight when carrying a payload. We assume the agents are connected to the payload through rigid attachments, essentially transforming the whole system into a larger flying object with ``thrust modules" at the attachment locations of the quadcopters. We investigate the optimal arrangement of the thrust modules around the payload, so that the resulting system achieves the best disturbance rejection capabilities. We propose a novel metric of robustness inspired by H2 control, and propose an algorithm to optimize the layout of the vehicles around the object and their controller altogether. We experimentally validate the effectiveness of our approach using fleets of three and four quadcopters and payloads of diverse shapes.