Please read the following documentation.

https://retropie.org.uk/docs/Mega-Drive-Genesis/#switching-emulation-station-to-the-genesis-logo

Very similar to my build (including the Mayflash), although I cut some grooves in the expansion slot to add some USB ports.

I wired the reset and power button to work as well, using a coupleof trimmed microswitches and GPIO pins, think I used the 'PiGirl' script to add them easily, then set the reset button as an exit emulator option, as I just couldn't configure that with a standard Mega Drive controller.

Thanks!

I find macs gave issues with Linux symbolic links on smb shares. They show up as blank folders. On the pie the genesis and mega drive folders are the exact same folder. Only a tag in Linux that makes the genesis and mega drive folders one in the same from the os point of view. Like alieses on mac or shortcuts on windows, but deeper rooted. It doesn't just point like the other two.
So do Everything in the mega drive folder.