Hi,
I would study existing PlayMaker open source games to get a feel of how things can be organized within your scene.
it also depends what UI system you will be using, it will greatly affect organization.
don't overthink this aspect, it's usually not really important when you start somethings, and you can always reorganise things as you progress in your project. It's actually pretty much always the case that you will have to refactor here and there, so get your hands dirty and dive in however you feel best here.
Typically, I personnaly use a lot of empty gameobjects simply like "folders" basically, and I name them oddly like "__MANAGER__" or "-UI-", just so that it stands out in my scene hierarchy that this is purely a structural item.
Bye,
Jean