If you do not have any skill, magic or perk points, the game just "erases" the lines in the save file, when you have atleast 1 point, it shows up in the save file.
And what do you mean "save the changes"? You mean where to actually put the files or how to push ctrl+s?
Well, you just open up the save file found in the folder, do the edits and ctrl+s?
Also, for the reasons that elude me, you do not need to actually edit any of the bottom ones of the "character sheet" found in the save file, only the first entries you've found in the save file, i do not know what the purpose of the second ones are.