Please go to the "Account settings" tab in the "My account" page. Make sure to select the correct country and enter your VAT number there.
The VAT number will be checked against the VIES database. Also make sure that you have selected the correct country and that the number is written on the correct form.
For Swedish customers, remember that we are located in Sweden, and thus VAT is handled as any other purchase in a Swedish store. You deduct the VAT when you do your VAT report.