There are some differing opinions, but what I do is edit /etc/emulationstation/es_systems.cfg and remove the .bin/.BIN files from the PSX entry. This was only the .cue files will show up in Emulationstation.
Yep – the link above covers that really well, the .ape are typically audio tracks that you can convert to .bin then merge back into a single .bin that the .cue file then has pointers to the various audio files.
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