Hi InsecureSpike,
I think what you are searching for are the files
emulators.cfg
in
/opt/retropie/configs/<name>/
Every system should have a file like this that lists the available emulators in the form:
<shortname> = <runcommand>
it will also have a line
default = <shortname>
which is the default emulator that is currently used for this system. You can change it to another <shortname> to change it, that is what the menu script does.