YITH WooCommerce Checkout Manager is a plugin that allows you to customize the checkout fields by adding, removing or editing any of them. You can take advantage of many types of fields.
The combination with YITH WooCommerce PDF Invoices & Packing Slips allows you to also edit the fields (VAT and SSN) that the PDF invoice plugin adds to the checkout.
Just make sure you have enabled and activated both plugins to make the integration work. No other action from your side is required.
To read more about the settings of YITH Checkout Manager, please, refer to the official plugin documentation.