Good afternoon, I have been selling products on Amazon for over 6 months, having always mixed selling between FBA and MNF, now I have been having problems with taxes and invoicing, mostly that my company has a Portuguese VAT registration number and just that. I activated Amazon's self-invoicing without really understanding what I was doing and they started to just issue invoices for the orders that I sent from Portugal and the orders that were from the Amazon warehouse in Spain were not issued invoices, due to the lack of a VAT numbers. So I signed up for the Balçaõ Único system and they still wouldn't issue it, now I'm having problems with Portuguese authorities and my accountant doesn't know what to do either.

Resuming , Amazon only issued me a few invoices with different VAT amounts(that i assume because of the country of destination), what do I do with these invoices and to whom and how much do I pay. In relation to the others, do I have to issue them myself?