Thank you for the response. I ended up figuring it out. What you posted was only part of the solution. What you posted was once you got Into the emulator Configuration settings.
To get to the needed setting screen, from the main screen of xbmc-emustaion highlight the system you want to setup, in this case NES, then press "Y" this will give you a pop up. Select yes and it will open the emulator without launching a game. Next select the rom you want to configure and press "X" this will bring up a screen that will allow you to change the type of controller in each port.