If you have integrated your invoicing software into Webshippy, Webshippy will generate the invoice with the same data content as the one that came from the webshop with the order (even if Webshippy's system may have a different one, as the information in the order will be the default). If the VAT content of the products in the order is not correct, you can change it in your webshop.
Although you can include consumer price and VAT content for products in Webshippy's system, this is only relevant if you add products to an order manually in Webshippy's interface. Of course, you still have the possibility to change the price and VAT content either by editing the order or by rewriting the basic product data.