Making the internal drive the default after booting from a backup drive
 

I'm guessing that it's not necessary to boot from an external backup drive to restore to the internal drive.

But having done that, what is the correct or best way to revert completely to the internal drive from that point on?

For example, if I run Firefox from the Dock, it would default to being run from the backup drive. If I start doing something like saving new bookmarks, those will end up in Firefox on the backup drive rather than the internal drive.

Is making sure programs run from the internal drive just a matter of clicking that drive's icon before running the program from the Dock -- or is it always necessary to restart (with Option key held down) and select the internal drive to make sure that happens?

Thanks.

You'd select the drive in the startup disk preference pane in system preferences.