Welcome!
The good news is that you can do all of that very easily in Scrivener!
[Edit - I see several answers came in while I was composing, forgive me if this has already been said]
I’m not at my computer right now and don’t have time to elaborate, but color coding both your binder items, index cards/corkboard/outliner etc is one of the best features if Scrivener (imho).
In the meantime, think about what is you want to color code. One method can only apply a single color at a time, so it would be most useful for something that doesn’t change within your smallest/lower level binder item- in your case that looks to be scenes? Ideas are maybe location? level of completion? Story line? - whatever you feel is most important to track visually with a unique color per binder item.
Keywords can also be color coded, and there is no limit to how many you create or add to a binder item.
Also check out the metadata panel - you can add dates, checkboxes, text, lists etc.
I highly recommend you refer to the users manual and the tutorial under “help” in the menu bar. This will give you an overview of how many ways you can keep track of anything. If you prefer videos, there are those too. 
