You can manage your documentation files in the same way as the other files of your projects.
Documentation files, like all other project files, are associated with a file type. The file type describes the various attributes of files of a particular type, including where these files are located (relative to the project directory).
You should store your project documentation files in a subdirectory of the project directory and version control them in the same way as your other version controlled files. You can then keep your documentation up-to-date by checking them in and out along with their corresponding source files, regardless of version or configuration.