If you do disk to disk clone, you will make an exact copy of the source disk to the destination disk.
BEWARE of booting from usb when the source drive is installed as well!
A modern OS uses UUID's (identifiers) to manage the hard drives. You are effectively creating a drive and partitions with the SAME UUIDS in the USB drive AND the local drive.
There are steps to manage this, but understand it could cause you issues. A simple way to manage that is make sure to simply disconnect the internal drive in the bios when you boot from USB.
OR
Boot normally, and add a virtual machine to the host and run your USB drive inside the host VM.
Also, there are some good videos (from other people) on using clonezilla on their webpage, I know one of them talks about identifying the disks and walks you thought the process of making the clones and restores if that helps any.