It is NOT intended to be used inside custom content feature code (maybe that is not what you are saying but just to be clear).
It is used by the setup page and the the routines used for creating new sites to setup default content when the initial site is created and when additional sites are created. Feature code only runs after a site is created and after an instance of the feature is added to a page.
The initial content system can be used to create a page(s) and add your custom feature(s) to the page when a site is created, but that is all it does.
There is only one page pre-configured by default and that is the home page and it is configured because of the presence of the configuration file
/Setup/initialcontent/pages/0001homepage.config
If you don't want it to create that page you can remove that file and add your own. Or if you are copying your files up there using post build event you could give your file the same name and then it would overwrite the default homepage config file with yours so that it only creates the pages you defined.
Any number of files can be used and any number of pages can be defined in each file.
Hope it helps,
Joe