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The easier way to delete a backup is to do it through iTunes. Open Preferences in iTunes, select the Devices tab. It will show you all your devices and their backups. You can select and delete them. There is only one backup per device. iTunes does not keep multiple backups (and most of us wish it would).
The numerous folders are just parts of each backup. If you drill down far enough you come to files full of the gobbledygook iTunes creates in order to minimize space, and encrypt the files (if you've got the option turned on).