A Portuguese work visa is only valid for Portugal. If you arrive in Italy first, you're considered to be on a "tourist" visa (i.e. a Schengen visa), subject to the 90 day restriction. But on a tourist visa, you are not "living" in the country at all. You're "just visiting."
If you're working in Portugal how are you living in Italy? I guess you could fly Rome/Lisbon twice a day. I've seen worse commutes. But other then that I can't understand how you could be working in one country and living in the other?