Is there anything special we need to do? Can we still use the electronic entry or do we have to use the regular line and get a special endorsement?
You should be able to enter the border normally using passport.
I would make sure to give them your golden visa and your passport to make sure it is counted properly in SEFs systems to ensure your time in Portugal in properly recorded.
Each time I go through I give them my passport and visa card. Only once was the visa card scanned. My attorney says as long as I have the passport stamps or Schengen passport stamps and boarding passes if arriving via another country I am golden. I save all receipts and enter my NIF on all purchases.