Backup nand will copy all of the console emmc/nand chip, including the user partition which includes all your game saves...
To modify Saves on PC>
Use a switch nand/partition/file system manager to extract user partition, pull your saves out of the correct folder from the user partition extract, back up/ modify/ saves,place the newly modified edited saves back to user partition extract folder... restore extracted User partition,encrypted back to console..
To backup Saves on Console>
on console use a Home brew application called checkpoint.. it is a save manager.
In your case only use cfw after you have a clean nand backup or wish to use cfw.
When you backup your console, make sure to backup the entire nand with hekate, and make sure to backup your BISKEYS..
Both very important, biskeys more important then anything else,so back them up first..