@greenhawk84 yes.
Add the line
lr-flycast = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-flycast/flycast_libretro.so </dev/null --config /opt/retropie/configs/arcade/retroarch.cfg %ROM%"
to your /opt/retropie/configs/arcade/emulators.cfg.
Move the rom to the roms/arcade folder.
Restart Emulationstation, click the game name in the arcade list, pull up the runcommand menu, select emulator for ROM, lr-flycast should be in the list, select it, and launch.
I assume you have or know how to set/activate runcommand. if not, go to config menu of emulationstation, select "run command configuration" and make sure "launch menu" is enabled.