My guess is that Custom Destinations is not stored anywhere until you write to it. As noted in the help files this is for advanced users only. I do see the module installed on both Free pbx 11 and 12 but cant find the config anywhere in /etc/asterisk.
But I would guess again that if the module is not installed
obviously you wont be able to drop down on the menu to select with in free pbx. However if you are skilled enough you could always include the file in Misc destinations or the appropriate directory to call the config leading to the script
But after all that nonsense i am curious to what kind of script your using and would like to learn this with you
Thanks
Take for example disa.conf will not appear unless you create example_disa with in the disa module