The incorporation of novel technologies in building and settlement design involves unique challenges, such as frequent design changes, the risk of cost overruns and the need to synchronize the work of different stakeholders who did not previously collaborate. This paper describes the development of a set of control and optimization tools that support the implementation of highly innovative energy technologies in the design of Net Zero Energy settlements. Three tools were developed and implemented. A cost control tool tracks the technologys initial costs during the design phase, so that any cost overrun can be easily recognized and treated. A change management tool allows the projects designers to identify, examine and discuss the implications of every proposed change in the design before the change is executed, and prevent deviations from the projects cost and energy performance requirements. A third tool supports a life cycle cost analysis of each technology and an identification of their optimal configuration. In response to a tight schedule and the uncertainty regarding the users exact requirements, an Evolutionary Prototyping methodology was adopted to develop the tools. They were implemented in a project involving the design of Net Zero Energy settlements in four different European countries.