VAT Invoice for amazon partnered shipping to inbound FBA Stock

Reports -> Tax Document Library -> Seller Fee Invoices

It will probably be in with all your other FBA fees for the month.

The invoice is not produced until around 7 days after the end of the month where the fee occurred.

If you are VAT registered and have given Amazon your VAT number then it is likely at the moment VAT will not be charged on this and it will be reversed Charge. From the 1st August VAT will be charged though as there is a change in the way Amazon treat VAT.