C2 actually makes it's own folder structure. The one you see when you save as a project. Then depending on the final export could change but usually project structure only matters on design/programming phase.
Then you also have internal folders on c2 editor. Here you better do as Alexixiv said before, make a subfolder for every area (sounds, music, graphics, backgrounds, etc). But also you should add more and more subfolders so you can track easily (and so your team) any file.
I usually divide my files into: Graphics/Enemies/Level1 or something like that. Sprites/Enemies/Generic and so for sounds, backgrounds. Nothing in the air.
Finally containers should be "thinked" as some dangerous but very handy kind of organization. Requires deep previous knowledge about how everything will work. But it pays in the end.
Foldering a project is a matter of your own sense of order. No one will order better your "stuff" than you.