place your scripts in the folder that you have designate in your es_systems.cfg
<path>~/RetroPie/roms/apps</path>
so in the aformentioned example they would be placed in a folder called apps in the roms folder. they’ll show up if you have the same extensions on your files as indicated by this
<extension>.sh .SH</extension>
so in this case they would be shell scripts- if they still aren’t running even if they show up you may have to sudo chmod +x yourshell.sh