controllers should be auto recognized by the game, but the way game maker reads the controllers is to assign them to one of several ports and then read inputs from that port. there is a setting in the menu under P1 Controller Remapping that allows you to set the port that is being listened to. I know the game can also be weird sometimes about controllers plugged in after the game has started up
On this menu you should see a name pop up when it's on a controller port with some device recognized, otherwise it'll just show the number.
