The best way to run Tiny Core on a hard drive is using persistent home and opt.
Include "opt=sda1 home=sda1" (use correct partition) in the bootloader.
You then don't need to backup anything in the home or opt directories, which is everything until you set up something which needs settings saved in another directory. For example if you set up a printer.
The best way to save settings then is by making an extension for settings.
http://wiki.tinycorelinux.net/wiki:extension_for_settingsIf you don't have anything to backup, also include "norestore" in the bootloader. So you will have added "opt=sda1 home=sda1 norestore"
If you want to use backup, edit /opt/.filetool.lst, delete every reference to home and opt (which is everything), and type in files and directories you want to backup.