They both do their job. PKGBackup does a bit more work and has a better UI in my opinion, but ultimately, if you just want to backup your tweaks, xBackup does the job just fine.
SSH/Rooting means that you access the root directory or the system files of your device, much like the "My Computer" or your "C drive" on your computer. It allows you to access the "behind the scenes" that's available from jailbreaking your device (you cannot/have limited root access when you're not jailbroken). You can most certainly use PuTTy to SSH into a device, but PuTTy would be to run commands usually. If you want file management, something like WinSCP, CyberDuck, iExplorer, iFunBox are all computer-based utilities that you can use to SSH/Root your device, allowing you to have an actual UI where you can see the files and drag/drop them like you would normally be able to on your computer.