Ok I figured this out, you need to choose the mednafen pce fast core and in the RetroArch menu go to Options-Core Input Remapping Option and assign one of your buttons to User 1 Mode Switch. I chose my select button. When in game, pressing select will enable a 6 or 2 button pad and a message will appear in yellow text on screen to show which is active each time a mode switch is made. Hope this is helpful for someone :)
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