I like drawyks layer idea and would maybe put that a little further. You can choose to add a new colour, which means adding a new layer. Every layer has basically the following parameters:
- colour and transparency (seperately for 3D-View and 2D-View)
- add to solution or not (flagging feature as described above), must be switchable until submitting
The switching for add or not enables you, to follow something and decide later, if that belongs to your cell or not. If you want to make it really fancy, you could add a "merge" function, to reduce the number of colours, if you're sure something belongs together.
P.S. I'd betatest