It's basically the same procedure for any joystick (N64 or otherwise).
Options->Configure Controller Plugin...
Select your controller from the dropdown list and then click on the various buttons on that window to map your controller's buttons/movements to the corresponding functions on the emulator. (IE, click the button labeled 'A' and then hit the A button on your controller. The text box between the label and the button indicates what key/button/movement is currently mapped to that function.) If the analog stick's range is off during game play, you may need to calibrate the joystick in Windows' Control Panel.