I always transfer anything I need long term out of scratch folders and keep them in a project folder in FCP7, I hate not having everything relevant to a project not located in the same project folder so the there is no risk of me messing up scratch folders. Never liked the communal location of working files in FCP7, glad that was cleared up in FCPX, though having to have all projects and events in the root of the HDD I really haven’t grown to like, it makes a mess of my own organisation/file-management. Should be able to select a sub directory for Project and Event locations. I can see why it’s probably done, but it’s too authoritarian for my liking, and not necessary, seems to be born out of mistrust of the users ablity to deal with their own file management.
I have done what you have said previously for backing up, but I tend to forget to do it in that manner, it just doesn’t slot into a smooth work flow for me.