@phillymadison
Drop the .cue and .bin files of the game into the segacd folder, yet I should advice you of something: Rpi2 and 3 has only 1GB of RAM and CD images has around 600mbs, as result the emulator can delay the loading of game and some sounds...
The best practices are extract the audio to wave format, keep the data into bin format and create a cue file (which contain the list of the files and also the type and which order those should be played), that way only loads the required audio file instead load the entire "CD", which improve the loading times of the sountrack a lot, the same can be applied to psx games as well.
The question is how you do that?
Pick an original CD or a CD image and open with isobuster (http://www.isobuster.com/)
Extract data into a folder
rename the data track into "name_of_the_game_track 1.bin"
rename the sound files into "name_of_the_game_track 2.wav", "name_of_the_game_track 3.wav", "name_of_the_game_track 4.wav", etc.
Try rename those in the right order.
Generate the Cue file by using the sega cue generator (http://www.racketboy.com/downloads/sega-cue-maker.htm)
Save the Cue file into the folder where the others files are, you can keep the name "game_of_the_game.cue"
Edit the /etc/emulationstation/es_systems.cfg and remove the ".bin" format from the platforms that uses CD's, to only show up the cue files on the game list, otherwise if you boot a bin file it wont load the sounds.
PS: it's important to rename the files, otherwise if you leave the files names simple as "track 1 and 2 and 3" it will overwrite with existent files from other games.
EDIT:
I forgot you also need BIOS and those are renamed differently according which emulator you use, you can find more about it here:
https://github.com/retropie/retropie-setup/wiki/Sega-CD