You can use all sorts of things, like 'dd' or 'cp -a'' or 'tar' - depends on what you want to do.
I have multiple disks and copy the entire /home directory across to the partitions on another drive. Key files are burned to cd or DVD of course.... I sometimes copy the entire OS across as well, partly as backup or mostly to go to a bigger partition
but mostly I install a new version of the OS on a new partition and keep the old while I set up the new one. But then I don't find most of the config is all that hard - though it can take a couple of weeks of part time tweaking to get every detail just right.
You probably don't need a backup of the OS that is 100% current, as long as you can boot it and it has most of the config.