You can develop your app so it uses generic settings, or settings that are specific to each phone. If you have phone-specific settings, you can choose to store them in the phone's config file, or have the user enter the settings via your app. This guide discusses how to choose the best solution for your app.
If you would like to have your application override one of the functions of the phone's built-in applications, the Application Redirection functionality will give you the ability. This guide walks you through the setup of the phone and your application to perform and handle the redirection.