So for the games that support it (ie: RE Revelations, MGS3D, Kingdom Hearts DDD), you use the extra R button.
But for everything else (ie: holding R to speed up the street passes) you still need to press the R button from the system, since it will not recognize the Circle Pad Pro's R button (which I find it dumb that it doesn't, but ah well...)
I understand that the additional slider and the ZL/ZR buttons won't work. But, why would the 'new' R button not work. It seems like all it's doing is sending an IR signal that telling the handheld that the button is being pushed.
I guess that the IR input recognition is coded into the game. Maybe it could be pushed to the actual console via update? I don't know.