If you are writing application help, you should work closely with the application programmer. The degree to which the Help System is integrated into an application is a design decision that you make collectively.
If an application and its help have very loose ties, there may be only a handful of topics that the application is able to display directly. This is easier to implement.
In contrast, the application could provide specific help for nearly every situation in the application. This requires more work, but benefits the user if done well.
It's up to you and your project team to determine the right level of help integration for your project.