I had set the notification bubble to bottom right, but when I set it back to top right, it's at the very far top right and overlaps with the panel. How do I set it to default?
You've most probably used NotifyOSD Config and the patched NotifyOSD, right? Open NotifyOSD Config and set "Positioning" to "Fixed".
You can also revert all the changes you've done from NotifyOSD Config via File > Reset.