Just to chime in here as well, I would also recommend the glupen64 core, runs much better for me than the default mupen64plus. All controller directions given above are true for this core also.
Also the newest nightlies are different, so assume this is coming in the next official update, but any changes you make while a core is loaded you can apply in the quick menu by apllying save core override.
As in the per core config in the gui is being replaced, with a simple core override in the quick menu.