Spain does not automatically upload VAT registrations and certainly not autonimo since every self-employed person is VAT registered and in Spain unlike other countries there is no registration limit.
The tax office does not really understand why a small self-employed person would be transacting business outside of the Spanish empire!!!
Anyway you need to complete modelo 036 and tick modificacion box 130 - Solicitud de alta/baja en el registro de operadores intracomunitarios.
Present the form for stamping at your tax office. I can't remember what you need to bring with you so to be on the safe side bring everything you have if you don't have identity card - so maybe in your case passport + NIE cert?
Then I think in about 7 days your VAT number will validate on the EU database.
http://ec.europa.eu/taxation_customs/vies/vieshome.do
I will shortly organise a competition on modelos and see who knows by number what each modelo is used for - the tax office only know what half of the forms are for ..... but no one knows what they are all used for ... it's quite funny if you ask what you should do next at the tax office - blank face and I don't know I just stamp this form!!!!
Another competition will be who can find all the little tax offices that exist - especially the ones hidden away - sometimes only 2 staff - but each office must have a security guard - so there's another job created.
Also now that you are all legal you won't have much time to run your business with all the little filings unless you engage a gestoria ........................
Word of warning don't employ anyone outside family - I'm being serious here.