Codex

The plugin does not allow you to override the form-checkout.php template from the theme files.
This is because it’s a customized template and if your theme already uses a different template, the plugin will not work.

Many users, however, would like to copy the template from the plugin folder and paste it into the theme, so it can be customized.
To override the template, then, add the following code into the functions.php file:
add_filter (‘yith_wcms_load_checkout_template_from_plugin’, ‘__return_false’);