There is a way to duplicate a core and make it behave like a completely different one, with a different settings folder, etc.
I asked for this some time ago and someone wrote a little program that allows you to do just that.
Here, download this: https://www.mediafire.com/file/3yz5g2slda3o24l/Core_Splitter.zip/file
This is what i used to duplicate the “Atarti800” core and make a second one named “Atari520” (to have different cores for the computers and the 5200 console).
By studying the .bat file (open it with with a text editor) you should be able to figure out how to duplicate other cores, it’s just a matter of changing the names.
This will also duplicate the .info files so you won’t need to do it manually.
I don’t use this anymore since you can now save everything “by directory”, including the main core options (which wasn’t possible before). But that’s when you want to use different rom folders (i have the Atari 800 and 5200 roms in different folders obviously). If you want to use the same rom folder though, this duplication trick is a better, cleaner solution than duplicating your roms.