This is an example, which would sync a backup of your /home/user/data directory to a mounted backup disk /media/backups with a backup directory data. Note that the destination does NOT end with /. This would delete all files in the backup destination that do not exist in the master source data.
rsync -av --delete --delete-excluded /home/user/data/ /media/backups/data
Use this option first to make sure it's doing what you want. Always use --dry-run when debugging your backup arguments the first time to make sure it's doing what you wanted/expected!! Otherwise you could for example delete all the data in your source if you get the sequence wrong. -v makes it verbose, which shows what is going to where.
--dry-run
rysync is very complicated to understand but very powerful but once you have the backup scripted so you don't forget it, it's a one time thing, then you just run the stuff.
I use rbxi to automate my rsync backups, but that's overkill for most applications.
rsync is one of the best unix type tools I have ever seen, the author is a genius (the creator of samba if I remember correctly), the chance of there being something technically better I'd put at fairly close to zero.
Note that if you have both backup drives mounted, you can simply rsync the main data to the first one, then rsync the first one to the second one, and you have perfectly matched data. Trying to unravel stuff with gui tools... well I wouldn't rely on anything like that for my backups is all I can tell you, if they are good, they are probably using rsync as their engine in the first place, if they are not good, they aren't, and I wouldn't trust them.
once you have your main data stuff done with rsync, it's usually a matter of only a few minutes to sync up to date, since it's done by changed chunks only. As an example, my main backup backs up about 1 million files, 400 gigabytes, give or take, and it takes only about 20 minutes or so to run through all that with rsync. Time spent learning this tool is time VERY well spent, as I indicated, I can think of few unix type tools that are better designed and implemented than rysnc, and it's learning time you'll never regret spending.