After having described the development of new models for the energy equipment used in industrial utility systems in the first part of this paper, this second part explains how such a modelling framework has been developed into an integrated methodology for the design and optimization of utility plants that exploits the flexibility of these systems. The different types of problems to be addressed (i.e., grassroots design, retrofit and operational) are identified in terms of their major issues and tradeoffs, giving emphasis to the fact that these tasks require a robust optimization procedure to handle industrial cases. Mechanical driver selection is incorporated in the proposed strategy. Several examples demonstrate the applicability and the potential of the suggested approach to provide significant economic benefits when applied to industrial problems.