I think I have a solution to the button mapping problems:
Touch Screen = Control Stick
Digital Pad = Digital Pad
Digital Pad + Select = C Buttons
L = L
R = R
Y = A
B = B
Start = Start
A = Z
However, since the Control Stick could be on the touch screen, you could swap controls for right or left handed play depending on the game
That could be the starting controls until the ability to bind new keys comes along if any release of such a emulator comes around.
However, I have a concern about where the Z button should be binded. I think it could because If you look at the Nintendo DS game called The Legendary Starfy (yes, Starfy), you can switch the controls so it uses Y, B, and A, which, in my opinion, is a great control method.