@bram279b What mitu said plus... you should just be able to swap joystick ports with the controller. It's built into the base mapping if you're using a SNES style controller.
If not, it should be your "A" button, whatever that is. That should toggle.
Try it with an easier game like Bruce Lee. Use the virtual keyboard as well as the controller to make sure you have it setup correctly.
The Virtual Keyboard in lr-vice64 also has a button to press to toggle joysticks,