What are the best practices for storing configuration?

This is the new core config onboarding. If you don’t have items under the core config ( homeassistant: ) in your configuration.yaml file it will provide a nice GUI to set name, location, timezone etc…

More here: 0.94: SmartHab, Watson TTS, Azure Event Hub

It has nothing to do with discovered integrations or manually configured devices.

Can’t help you with the automations editor. I don’t use it.

I use names/entity id’s that help me know what I’m referring to when manually creating automations and scripts. For entities that don’t support name: or friendly_name: or icon: I set these in the customization section. For use in the front end I sometimes simplify these names. e.g I have a lot of temperature sensors so to distinguish which one is which I name them Room Name Sensor Type. In the front end in a card that has the room name in the title I use lovelace to drop the redundant information and make the display cleaner.

Not sure what you are referring to here. Can you clarify with a screen shot?

This is a matter of personal preference. I don’t find the automation editor capable enough for my liking and I don’t like the way it mangles YAML from human readable to alphabetical order. So I don’t use it.