[dnanian]

I try to make the procedure clear in the User's Guide -- let me suggest that you take a look at Section 9 & 10 (p25/26). But, basically, you'll boot back to the original drive and apply the update (or install the apps) there.

There is a way to "clone back", but it's an advanced operation that -- if done incorrectly -- can cause you to lose your original volume. Unless you're feeling terribly confident, I wouldn't do it. (You can find instructions elsewhere in the forum.)

If you're backing up to an external, always back up the ORIGINAL volume. There's no reason to back up the Safety Clone, since your user data is on the original drive.