I think there are mainly 3 options. Yours is a bit strange. Other than start and select, I would choose one of these:
C D Regular NGCD pad
A B
B C D Similar to original stick
A
----D Uses the 3 main, bigger buttons
A B C
I'be never tried to modify a genesis 6 buttons pads, although I like that controller a lot. When you do it please post here whatever info you can about it, many people will appreciate it.
By the way, where are you going to solder the wires, in the button's place in the PCB or in the chip?
Good luck.