Fuel cells are an attractive alternative to other energy conversion methods because of their efficiency and energy density. Unfortunately, the high expense and limited durability of catalysts in common fuel cells has slowed their commercialization. The limitations of current anion exchange membranes (AEMs) may be minimized by improved design and material optimization. This work aims to improve the understanding of fuel cell AEMs from a fundamental perspective through multiscale simulation techniques. Studies on hydroxide anions in relevant AEMs reveal the importance of explicitly including the physics of proton shuttling to properly describe the solvation and transport of the ions in these systems. These results are in turn bridged to a mesoscopic simulation methodology that incorporates the morphological features of the membrane, leading to a better understanding of the coupling of domain structure to charge transport processes and its affect on ion conductance properties.