Do you mean they would take the "hill track" (now out of service) to get to the Bordentown branch?
I guess as noted the doodlebug could also have gone the otherway to Monmouth Junction and Jamestown, etc.
Did the Nellie Bly take the main towards Philadelphia? If so did it have to reverse at Frankfort Junction for Delair bridge or was there a wye?
At the time, it was the Bordentown Branch; indeed, it went up a hill.
The doodlebugs ran three ways out of Trenton: Camden, Phillipsburg and Red Bank. Given that this one is sitting at the west end of the eastbound platform, it was probably a Camden car.
The Nellie Bly operated via the Bordentown Branch as did the Camden service and a commuter train to Philadelphia. They went their seperate ways near Delair.