It's a bit finicky and doesn't work for all controllers, but here's how you set it up: Make sure the gamepad is connected, then open the game. Press F1 and then select the tab that says "Gamepad."
The game will ask you to input letters to corresponding gamepad buttons. Here's a quick rundown of what each letter does:
Letter A: Hold down to walk slower (or to run if Auto-Run is turned off)
Letter B: Cancel/Menu Button
Letter C: Confirm, talk, inspect
Letter Y: Skip Text
It may take a little trial and error to get this all working to your liking, and some gamepads just don't seem to work. Sorry for the inconvenience and I hope this works out okay!