When you invoice subscriptions correctly, the prices will be calculated automatically. Before you create invoice rows for subscriptions you should make sure that the price lists for subscriptions are correct. Note that the price list has to be correct even before the subscription is even created!
Via Administration > Subscriptions: Sort the customers using the filters > mark the customers > Choose action > Create invoice rows.
Via the customer page: Go to the customers page > click the shopping-cart icon to the right hand side of the Subscription > write an invoice row description > Choose a VAT and if you want to add a discount > click Next > double check the information > Create invoice row.