The NCrunch project configuration settings are applicable to individual projects, and will be used by these projects for all solutions that they are a member of.
Project-level configuration settings are stored in .v3.ncrunchproject files adjacent to their respective project .proj files.
You can modify a project's configuration through the project nodes accessible in the NCrunch configuration pane (by choosing NCrunch->Configuration).
The NCrunch configuration pane supports multiple selection when applying configuration settings to projects. This makes it easy to assign a configuration setting to a range of projects at the same time.