Thanks for the response everybody. I should've have looked for the other entries but instead I just started typing as the ideas occurred to me :(

There lots of ways to do the layering approach and the suggestions people have made are really good. I guess the ideal approach would be unobtrusive and yet give the ability to browse the scene, select elements, group elements, ungroup them, assign basic materials, rename, lock/unlock to prevent accidental editing.

As I said before, this is great software and very easy to use with my tablet.

And V2.0 looks really stable so far - the CPlane is really very useful.