Hi Eden - except for the pages themselves, "General flow" of an application usually relates to the relation between the pages and to the end-to-end experience of a user in your application.
You can look at it as some kind of a "How-To-Use" guide for your application.
For example, let's say your app requires a login and registration of a user. An example flow would be:
- User enters the website, reaches your home page (Home page screen)
- If has no user, registers (Registration screen)
- Logs in (Login screen)
- Performs a series of actions in the website (Various screens)
- Logs out (Logout button)
Hope this helps! :)