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Personally, I'm planning to use QWE ASD ZXC, but also allow 789 465 132 mapped to the same virtual "buttons", but I assume there'll be no problem if I also map those same buttons to work with a controller's D-pad and ABXY buttons (+ the back button for button #9)? I've got a friend who prefers playing EVERYTHING with a usb controller.

So in effect there are 9 buttons for the game, but 3 different ways you can choose to map those buttons, I assume that'll be fine?

That sounds perfectly fine