If what you want is "mirroring", i.e. make destination directory tree identical to source directory tree, then the command line is really simple. You need the option -a and the option --delete if you want to delete files in the destination that do not anymore exist in the source. For example:
rsync -a --del /home/user/source/ /home/user/backup/
Setting this up for the first time, you might prefer to omit the --del to see if the copy goes into the right destination. The --del option could be very dangerous if you mistakenly swap source and destination.
That said (we are somewhat off-topic) I do like nautilus for daily copying work nevertheless.
In fact, when copying a directory over, nautilus asks first if you want to "merge" or "merge all" (i.e. copy into the destination directories) and then asks whether to replace or not already existing files. Using the "skip all" option, it will only transfer files and directories that do not yet exist in the destination. I tested on a quite large volume of data, and because both prompt comes early in the copying process, I do not see the issue.