Cloning Macbook Pro HD to external HD and still using it
I have had good luck by booting into recovery mode and using Disk Utility to clone the drive before doing major OS X upgrades.

The steps:


Plug in your USB drive.
Boot your Mac into recovery mode by holding down command+r from the start of boot.
Once the recovery menu comes up, select Disk Utility and click Continue.
Select the drive you want to clone and click the "Restore" tab.
Drag the destination (USB) drive to the "Destination" field.
Click "Restore".


Once the process is complete, reboot the computer and hold down alt / option and select the drive you've cloned to. This is good to be sure it's functional before upgrading OS X on the main drive. Some software will detect that something's different (Dropbox, Photoshop) and may ask for credentials or to be setup again. But the vast majority of software just works as if nothing happened.