You can change your VAT settings by going to "Settings", "Company settings" and "VAT". If you created an invoice without VAT then you need to turn VAT on, delete the invoice, and do it again.
Withholding tax is when a sum of the invoiced amount isn't charged the customer, instead this amount is paid by the customer to the tax office. If you use withholding tax you create an item and set the VAT to 0%. You add the value of your withholding tax as the price with a minus sign "-" in front.