Let's call your personal files P and call Windows W.
Synctoy is a file by file back tool used primarily to back up P rather than W. I've never used it, but applications of that type are not likely to back up all W files even if you attempt it. They may not even back up absolutely all of your P files--for instance if some P files are open or have an extremely long path.
You can normally investigate the log file generated by a backup program to get an idea of what it did not back up and you may even learn why.
Synctoy is not a good candidate to back up the registry or your INSTALLED programs. I wouldn't expect it to back up the registry at all.
Backing up W (including installed programs) is best done with an imaging application such as the one built into Windows or Acronis or Macrium Reflect.
If you make an image of C and then restore C, the registry of the restored C will be identical to the state of registry at the time you made the image. You can't restore just parts of an image, but some imaging applications will let you root around in them to recover individual files--without restoring the image.
P would normally include all of your documents, pictures, email, music, video, browser bookmarks, and the uninstalled versions of downloaded programs (anything you don't have on an installation disc).
You need to discover in what folder each of those things lives on your hard drive and then direct Synctoy to those files/folders--rather than to Windows files.
It can be advantageous to keep your P files on a separate partition for organizational purposes. If you instead keep everything (P and W) on the C partition, then any image you make will include both P and W. You will likely find that keeping P file backups in an image can lead to problems---the image may fail or you may not be able to easily access your P files within the image.