This paper develops a distributed parameter model for a multiple component structure morphing, flexible wing aircraft with a n trailing edge rigid flaps. Using a set-theoretic adaptive control approach that utilizes restricted potential functions, we implement a decentralized command following control architectures for each active module (flaps) such that these modules can effectively perform their tasks with user-defined strict performance guarantees in the presence of unknown physical interconnections between modules (wing and flaps) and module-level system uncertainties.