The app level Configure URL is called when an app user clicks the gear icon from the app in the app catalog. The app is expected to provide a URL for a configuration page for Eloqua to display in a module, similar to a Configure URL in a service. App level configurations will be saved by the app, so there is no action other then the app collecting information that'll be needed at the app level. Eloqua with GET the specified Configure URL.
The Uninstall URL is called when your app is uninstalled by the user. Eloqua will send a POST request to the specified Uninstall URL.
See App level URL template parameters to view available URL template parameters for each URL.