Hey bud, we are in the same boat. Run jstest and write down all the inputs and corresponding numbers. Use your Rii to hit f1 while in lr-mupen64plus-next to open the retroarch GUI and scroll down to "controls", then remap everything according to you jstest results. This got me to the point where every button works except for c-up and c-right. Please let me know if you can get any further or if you've already solved the issue.
@kill if you have matching controllers or encoders you never have to configure player 2. Both players share the same config file. After you setup player one if you want player two working immediately in emulationstation just restart emulationstation. Retroarch emulators dont need a restart to have player 2 already working in it. You can create problems trying to find an issue with encoders wiring between both players if you setup player 2 as it overwrites any configuration you setup with player one.