You don’t need to use libraries. Like you, I am highly organized and don’t use them. I have even used the tutorials on this site to make “libraries” largely disappear from Windows Explorer. I save my stuff directly to the desired folder, never mind libraries.
You are correct. A bona fide backup program will overwrite ONLY new or recently modified files. Therefore---the first backup takes a long time. All subsequent backups rarely take more than a minute.
The way to “save” all of your (installed) programs is to make an image of the C drive. Windows backup can do that, but I prefer Acronis or Macrium. You can get at least one of those two without paying. Such an image would also contain your “Dad’s Files” user folder if it is on the C drive, but I urge you to do separate and distinct “file by file” backup using a dedicated backup program such as Cobian, Karen’s Replicator, Second Copy, or Sync Toy. Any of these applications can also back up your email. The location of your email varies depending on what email application you use.