This doesn't necessarily apply to Newark, but I recently accompanied a friend to Heathrow to check in for the CO codeshared, VS operated service to JFK. Asked about checking in somewhere other than the standard coach line. First response was no (from a very unfriendly agent at the service desk). So we proceed to the economy line where the ticket is checked while waiting(along with a quick show of the elite card). After explaining the situation, the agent apologizes (at length) for the confusion and personally escorts us to the premium economy/upper class area where we had a mere two people in front of us. Much better than the wait of 40 or so people in front of us in the other line.

I would imagine Newark would probably have the same policy. As FCTSTY said, just act like you belong and be friendly to the agents. You should be fine.