Long answer
Did you try to launch nintendont? it asks you to select the device to use, select USB or SD with your controller D-pad up and down, then press A.
When you see the game list, at the top of your screen you will have some texts too, and some of this text tells you "Press B to access the options".
so, at this precise moment: press B to access the option screen. If you press A instead of B, the game where you have the cursor located at will launch and you will not be able to access the option screen anymore. so be very careful to access the option screen correctly. when you access the option screen, you will see text printed on your screen again, this time with different option name. One of the option's name will be "Memory card emulation", press the d-Pad down on your controller multiple times until the cursor telling you which option will be affect by your decision reach the option you want to edit. Press A button on your controller and the option will change, press A again and it will change again until it's back to initial value.
Stop pressing A when you see the text corresponding to the option you would like to use, then press B to go back to the game listing....
Really, users need tutorial to edit an option ?
Do you need me to tell you how to play the game too?
Short answer:
Launch nintendont and edit the options!