The current active track will remain active, but it will not go under the bridge. It will bear to the left as the connector track to SEPTA (known as the "Blueliner Connector"). The area will look much as it did before the work, except two tracks will be passing under the bridge as opposed to the one before, and both tracks will be able to handle stacks.
As for the entire project, much work remains. Many bridges have to have clearance work performed, including Cottman Ave (which is currently being reconstructed, but not to clearance height; apparently after the bridge is finished CSX will go back and undercut the track). The most challenging projects include the trench just east of CP Nice that goes alongside Wayne Station (the track passes under some streets-like Germantown Avenue-whose bridges can't just be rebuilt, BUT the trench is lined with concrete), and the NS overpass just north of Woodbourne station. However, it was said CP Nice would be difficult, but they made it seem rather easy.
Also, they have begun laying down one if the other tracks at CP Nice.