This research focuses on developing a comprehensive framework for designing and modeling experiments in the presence of multiple sources of competing prior knowledge. In particular, methodology is proposed for process optimization in high-cost, low-resource experimental settings where the underlying response function can be highly non-linear. In the first part of this research, an initial experimental design criteria is proposed for optimization problems by combining multiple, potentially competing, sources of prior information--engineering models, expert opinion, and data from past experimentation on similar, non-identical systems. New methodology is provided for incorporating and combining conjectured models and data into both the initial modeling and design stages. The second part of this research focuses on the development of a batch sequential design procedure for optimizing high-cost, low-resource experiments with complicated response surfaces. The success in the proposed approach lies in melding a flexible, sequential design algorithm with a powerful local modeling approach. Batch experiments are designed sequentially to adapt to balance space-filling properties and the search for the optimal operating condition. Local model calibration and averaging techniques are introduced to easily allow incorporation of statistical models and engineering knowledge, even if such knowledge pertains to only subregions of the complete design space. The overall process iterates between adapting designs, adapting models, and updating engineering knowledge over time. Applications to nanomanufacturing are provided throughout.