I finally got the Amiga emulation to work! This is how I did it.
Since I had Amiberry already installed, I removed it and its config file from /opt/retropie/configs/amiga (all .cfg files in that folder).
I installed kick13.rom, kick20.rom, and kick31.rom with the correct CRC in bios/amiga. I used the
wiki to get this information.
I then installed Amiberry from source. I did it by launching Retropie Setup from Retropie. I selected Manage Packages->Optional Packages. I selected Amiberry and chose to install from source.
Back in Retropie, I restarted Emulation Station.
I selected Deluxe Galaga (which, of course, was stored in roms/amiga) and it worked! I was having a problem with it not saving the high scores. However, I discovered that if I pressed ESC from within the game, it exited to DOS and then would save the high scores.