Where do I add custom php or javascript?

For scripts like Adobe fonts, or other third party  integrations, add those to Divi > Theme Options > Integrations > In the correct field.

For other scripts, for the purpose of functionality, add those under Appearance > Theme File Editor > script.js

For php snippets, add to functions.php or the Code Snippets plugin by Code Snippets Pro.

Make sure to properly label / comment all customization with what they are / where they are in use.