There are plenty of tools to help you backup your system. My personal favorit is rsync
To back up your home folder
rsync -a --delete --quiet /home/User /path/to/HDD
-a
indicates that files should be archived, meaning that most of their characteristics are preserved
--delete
means files deleted on the source are to be deleted on the backup as well
It can be done using ssh as well just add -e ssh /home/User user@server:path/to/backup
(if the dedicated HDD is running on a separate server such as mine is)
As a full system backup (which I'm failry certain is what you're looking for)
rsync -aAXv --exclude={"/dev/*","/proc/*","/sys/*","/tmp/*","/run/*","/mnt/*","/media/*","/lost+found"} / /path/to/backup/folder
Using the option -aAXv
ensures that all file permissions, ownerships, links, mod times, ACL's and extended attributes are preserved!
I personally have a script to backup my home folder weekly and then zip it and send it to my server, and once a month I will do a full system backup and send it to a different more secure server.
You may also be interested in checking out --parial
flag! For completeness though here is the man page https://manpage.me/?q=rsync