Better yet if you are trying to get the genesis theme instead of the megadrive theme- the easiest way to do it is change the es_systems.cfg file under megadrive. You can keep all of your roms in the megadrive folder and everything else the same- all you have to change is the theme.
/etc/emulationstation/es_systems.cfg
change it to look like this
<system>
<name>megadrive</name>
<fullname>Sega Mega Drive / Genesis</fullname>
<path>~/RetroPie/roms/megadrive</path>
<extension>.smd .bin .gen .md .zip .SMD .BIN .GEN .MD .ZIP</extension>
<command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ megadrive %ROM%</command>
<platform>megadrive</platform>
<theme>genesis</theme>
</system>