Hello, I don't know if anyone can help you with this, maybe try to share your project?
Otherwise try to be more precise, to explain better?
I didn't understand everything, but I think you want to make a combat system and you're asking if you need to make a scene for each one?
The answer is obviously no, use a single layout, use a layer, put your element on it and make it appear or disappear when you want, thank goodness layers exist!
Remember to disable certain things, like character movement, inventory etc., I don't know.
You can also change the order of layers, even in-game!
For example, move one layer in front of or behind another.
I don't know what more I can do for you, good luck!