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davejacaI have a video that goes into this, check around the 4:40 mark: https://www.youtube.com/watch?v=lh0n5PWN2lI
What you need to do is access the F1 menu in the emulator, go to settings then input settings -joypad mapping. Select User 1 Bind All and go through the button assigning. It wont actually ask for n64 buttons but I can tell you that the C buttons are mapped to the right analog stick; so when it asks for Right Analog Y- (Up) you would press the C-Up key on your gamepad.
Hope this helps, let me know how you go.