If you want to be able to restore the machine completely, with everything installed and configured, then yes you have to backup everything. There's generally two ways, file-level backup where you'd use something like rsync, tar, etc. and block-level where you'd backup the whole partition/disk using something like dd, clonezilla, etc. The latter is the easiest to restore but it's a bit of a pain to backup because the system generally has to be offline, booted from alternative OS. The forner is a bit more difficult to restore but not by much, and it's so easier to backup. You can do it while the system is live. I'd probably try that first. Find documentation on backing up a complete root filesystem with rsync/tar and you're good to go. Some ideas. It's typically a single command which can be run on a schedule.

The built-in GUI backup tool is generally intended for your own user data. In order to be able to backup other things it'll have to run as root or be given caps and that might get more complicated than using straight rsync/tar.