There are a couple of permissions that don't behave like normal and dangerous permissions. SYSTEM_ALERT_WINDOW and WRITE_SETTINGS are particularly sensitive, so most apps should not use them. If an app needs one of these permissions, it must declare the permission in the manifest, and send an intent requesting the user's authorization. The system responds to the intent by showing a detailed management screen to the user.
For details on how to request these permissions, see the SYSTEM_ALERT_WINDOW and WRITE_SETTINGS reference entries.