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In the future wireless communication environment, many radio access technologies will coexist in the same or border areas to provide users with ubiquitous access. The heterogeneous infrastructure makes reconfigurability an important characteristic which is very necessary in the mobile terminals. Moreover, the reconfiguration technique is also introduced to the design of protocol stack to meet the ever-changing link conditions and service requirements. Hence, in order to facilitate the realization of the protocol reconfiguration capabilities, a component-based protocol architecture is introduced by end-to-end reconfigurability (E2R) II project. This paper focuses on the supply of a customized protocol stack for each application according to the communication environment. To achieve this goal, an evaluation mechanism for protocol components is proposed. Besides, we put forward an optimization scheme that finds better protocol components from the network-side library to replace ill-suited ones running in the current system. The major advantage of the proposed protocol management schemes is that users may enjoy a better quality of service due to the protocol reconfigurability.