To make your store automatically charge the proper VAT amount to your customers, enable the Automatic tax rates on the taxes page in your store Control Panel. 

Your store calculates the tax rates automatically based on the store and customer's location and includes VAT into product prices as soon as the customer location is detected. At checkout, the customer will be charged a proper VAT rate according to country and regional tax rules. We also stays up to date on the current VAT rates, so when the rates are changed, your store will automatically use the new rates with no actions required from your side.

NOTE: Only standard VAT rates are supported by the automatic calculation scheme at the moment. If you are required to charge reduced rate or have zero-rated products in your store, we recommend disabling the automatic rates and set up manual tax rates. 

If you sell goods to another business and these goods are sent to another EU country, you do not charge VAT. VAT rules also require you to save customer VAT number and make sure it’s a valid EU VAT number.

To enable VAT reverse charge for B2B sales in your store, open the taxes page in your store control panel, scroll down to the Settings section and enable the “Ask buyer VAT ID number at checkout” option. 

It will add the VAT ID number field at checkout and apply VAT reverse charge when necessary. The customer VAT number will also be saved in the order details for your future reference.
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Please find the instruction here: http://knowledgebase.webydo.com/the-webydo-store/settings/how-do-i-edit-my-stores-invoices