This. This is what makes Crashplan a backup program, and Karen's software is not. It's the same reason I urge my clients not to treat Dropbox as a backup program.

Let me tell you how I would back up your computer if it were mine:

1- install Crashplan
2- choose the drives/data I want backed up
3- choose the location(s) to back up to

There's honestly not much of a reason to get more complicated than that.

This is how I've set up Crashplan for almost a hundred users over the past few years. All of their data is seen by Crashplan. All of their data is stored in at least one other location (some opt out of the cloud and only want one drive). All of their data can (fairly) easily be restored.

At the end of the day, I think you're still trying to force your previous way of doing things onto a new way of doing things, which doesn't usually work well...