In most cases, custom code to expand various plugins is added to functions.php in the active theme. And, that is just an awful way to add custom code for many reasons: that code is not related to the theme, so why add it to the theme. And, if you change the theme, you need to copy the code over.
The best way to add the custom code is by using Must Use Plugins. WordPress supports Must Use Plugins or mu-plugins since version 3.0, and they are the best way to add custom code to WordPress for the purpose of tweaking. Must Use plugins don’t need to be activated, WordPress will load them always.
Make sure that your website has a folder called ‘mu-plugins‘ in the ‘wp-content‘ folder, and if there is no such folder, make it. Once you have that folder, create a new PHP file in that folder. For example, make the empty file called ‘my-custom-code.php’. When empty, this file needs only to have php opening tag:
<?php // add custom code here //
You can add multiple files, and even name them according to the plugin you are adding custom code for to better organize the custom code you use.
When you need to add some tweak, function or any other PHP custom code, add it in this file, just like you would add it to the theme functions.php file.