Yes, you can boot and run your computer from the external clone in the dock. What I do is keep and archive a clone of the current system (10.6.8 was a very stable OS), then clone another drive and update that to the new OS for testing before cloning that to the internal drive. That gives me a chance to see how well the OS plays with all my apps first, then when I'm satisfied, I clone that to the internal and already have a current backup of the new system. Admittedly it is a cautious approach, but it has kept me out of trouble for many years.