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the images that the app loads are all from a single folder, so you can just put your images there, but when you’re editing the die faces you’ll still have to apply them one at a time.

Detailed docs are here: https://sophiehoulden.com/dice/documentation/customising_dice.html

Should I put images into their separate folder inside that folder, for better organization? Or will the program not recognize that?

Honestly, I can’t remember! I’m not at a computer right now so I can’t check, but even if it does make a difference it will probably only affect the order they are listed in. I’d recommend doing it that way just to keep your folder organised but it probably doesn’t matter too much beyond that.