Carry-on bags on a CRJ550

I am scheduled to fly from EWR to ALB. This flight uses a CRJ550 aircraft. I am arriving in EWR via an international flight and then taking this flight to go to Albany. I did not book the international flight and the domestic flight together. I was initially planning to take the Amtrak train and then realized that the flight, after using the available miles I had, was cheaper than the train. I am going to have a significantly large duffel bag as a carry on bag. I am worried that due to the small size of the aircraft, United might ask me to check-in my carry on bag. If this happens, would I have to pay for the carry on bag that I would have to check-in ?