How do I change the default sound for Reminders in El Capitan?
You were on the right lines, but the wrong location…

System sounds are in /System/Library/Sounds/ it's only user sounds in ~/Library/Sounds
Replace the Basso.aiff in there with your custom version [bearing in mind this will replace Basso in any other system alert that uses it too]  

It will be the same for Calendar alerts - except there you can define which system sound to use, so if you did need a separate custom sound in there you could apply the same logic to one of the other system sounds in the Library folder.



Note that in El Capitan you would first have to disable System Integrity Protection before you can modify the Sounds folder…


  
  Reboot your Mac into Recovery Mode by restarting your computer and holding down Command+R until the Apple logo appears on your screen.
  Click Utilities > Terminal.
  In the Terminal window, type in csrutil disable and press Enter.
  Restart your Mac.
  
  
  Revert the same way using csrutil enable