Intermodal trains run in and out of Port Newark and E-Rail. Port Newark is a CSAO Yard and most of the jobs within the yard are CSAO jobs. CSX and NS both bring trains into Port Newark while NS has built its own facility further down known as E-Rail. Some trains leave from and terminate there while others go to PN. Most of the power from NS is stored and most trains are made up in E-Rail though, while you see alot of CSX power sitting in Port Newark.
The Geeps ad SD40-2's you see in PN are most likely CSAO crews putting the intermodal trains together for CSX and NS.