Alitalia MilleMiglia - Will AZ in Newark check in a connecting domestic flight on another reservation?

Flying EWR-FCO Saturday evening (Magnifica Class) and have a connecting AZ flight FCO-VCE book on a seperate reservation code (booking Domestic through the Italian website saves a ton of money). Will AZ staff in Newark check me in on the connecting flight (with seat issue) and book our luggage through to Venice?

Also, on a slightly related question, which lounge does AZ use at Newark?