moebios, you only need to drag your objects to a single layout, even if you use the object in multiple layouts. The purpose of putting the objects in the layouts at least once (even if you don't need it in the beginning) is so that the C2 game engine knows what the initial values are for the object, i.e. the values in the properties bar.
For organizing, I just group like things together. And, I've put the objects outside of margins and it still works. In a future project, I've been thinking about putting all the objects in a layout that is never shown to the user. That might be the best way to organize the objects and keep them out of your way.