The project files are used to store project specific settings. These settings are:
include folders
preprocessor defines
It isn't recommended to provide the paths to the standard C/C++ headers - Cppcheck has internal knowledge about ANSI C/C++ and it isn't recommended that this known functionality is redefined. But feel free to try it.
As you can read in chapter 3 in this manual the default is that Cppcheck checks all configurations. So only provide preprocessor defines if you want to limit the checking.