In general use for backups I use rsync -avhW source destination
This produces a good copy preserving the things I care about. You might want to replace v with P to show progress.
The Arch wiki recommends this for file system cloning
rsync -qaHAXS SOURCE_DIR DESTINATION_DIR
That should copy almost anything exactly. It will even copy things like device files and hard links. This is probably more like what you want. Replacing q with P or --progress should give you some feedback.