This is an old Question but recently Android has a support for Bubbles. Bubbles are soon going to be launched but currently developers can start using them.They are designed to be an alternative to using SYSTEM_ALERT_WINDOW
. Apps like (Facebook Messenger and MusiXMatch use the same concept).
Bubbles are created via the Notification API, you send your notification as normal. If you want it to bubble you need to attach some extra data to it. For more information about Bubbles you can go to the official Android Developer Guide on Bubbles.