I think that depends largely on what’s easiest for you. A lot of users have requested more organizational features, but they may or may not be on the Trello roadmap.
The easiest way to do that is probably to combine function/behavior extensions with external event sheets. You can also use external layouts for things like the GUI with a corresponding external event sheet, which can then be linked to any scene you want. As far as I know, there’s no other way to make anything inherit from other scenes.
Yeah, unfortunately, there’s no way around having to make some changes to every level separately, at least when it comes to unique settings for variables, sprite animations, etc. In some ways it is easier to just copy a scene and make small changes than having to redo it all from scratch.
For this one, there are several other members who are more knowledgeable in this area.
You might find more specific documentation on that here though:
I’m not quite sure about this. I know that you can add hitboxes to the regular sprites, but I haven’t worked with panels much.