What swung me over to Nova was it implicitly tells you up front that it will save home page screens complete with all folder information to a storage location of your choice.
I have found that it will:
Save a backup to:
Share => Brings up a list of ways to share/store the file. On my S5 it shows, Evernote, Hightail, Blue Mail, Bluetooth, Drive, Email, Gmail, Wi-Fi Direct.
..... so far I have only used Blue Mail and Drive and it worked great with both of those.
Device Storage No way to define where it goes, and can't find it with a file manager either, but it does save it and Restore can see the saved files. They are hidden from a file manager though.
Document Storage Saves it to the SD card. at least it did for me. The first time I did this it showed me the SD card as an option and then it also allowed me to create a Folder. I did and called it Nova Backup. Now it don't ask me anymore, it just saves it to that folder on the SD card.
I have to say that I am impressed with Nova's backup and restore capabilities. It also has a much easier way of assigning which Home Page is the one that the Home Key button will access.
I now have multiple copies of my Home pages backed up all over the place. On the phone, on the SD card, on my PC and in the Cloud on Drive.
So, a three step process to clone your phone from a Factory Reset:
1) Kies 3.0 it repair it and get it going again.
2) Super Backup will restore all of your $$ paid apps and data
3) Nova Launcher will restore all of your Home pages