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Patched-grid algorithms for the analysis of complex configurations with an implicit, upwind-biased Navier-Stokes solver were investigated. Conservative and non-conservative approaches for performing zonal interpolations were implemented. The latter approach yields the most flexible technique in that it can handle both patched and overlaid grids. Results for a two-dimensional blunt body problem show that either approach yield accurate steady-state shock locations and jump conditions. In addition, calculations of the turbulent flow through a hypersonic inlet on a three-zone grid show that the numerical prediction is in good agreement with the experimental results. Through the use of a generalized coordinate transformation at the zonal interface between two or more blocks, the algorithm can be applied to highly stretched viscous grids and to arbitrarily-shaped zonal boundaries. Applications were made to the F-18 aircraft at subsonic, high-alpha conditions, in support of the NASA High-Alpha Research Program. The calculations were compared to ground-based and flight test experiments and were used as a guide to understanding the ground-based tests, which are laminar and transitional, and their relationship to flight. Calculations about a complete reconnaissance aircraft were also performed in order to further demonstrate the capability of the patched-grid algorithm.