Proper way to use plugin functions in functions.php

The active theme’s functions.php is included on the backend because a theme can be configurable from the backend.

If your theme depends on the functions of a plug-in being available, then you must either make sure the plug-in is always available or make your theme robust enough to handle situations where it isn’t.

You could put all of your theme’s functions that need the plug-in’s functions into a separate php file that is only included when the plug-in is active. This would make it easier for you to deactivate the plug-in for short periods while you make other updates.

So in your theme’s functions.php you could add:

if (function_exists('plugin-function-name'))
{
    include 'path/to/functions-that-need-the-plugin.php';
}

Then you only have check if function exists once, and the theme and backend will still function when the plugin is not available.