Here you will always find help from everyone, as far as possible.
But, doing a quick search beforehand doesn’t hurt. Or maybe try something that has already been answered, even if it is old.
RetroArch doesn’t care how you have the files when you make game lists, you can have everything together. Or you separate it in folder like the image. The only thing that matters in this case is to have the cue or chd in one folder and the m3u in another.
The only thing that is not going to change in the short term, are the multiple disk sets, maybe in the future it will be possible to compress the images in a zip like in PURE.
And if you don’t hit the Reply button, I don’t get the notification that you replied to me.