Another way you can model a vertical drop is to define the drop as a junction rather than a pipe. Connect the two junctions with a transfer pipe. However, the way you defined it should work fine.
Note that you cannot vary the area of the junction--it is assumed to match that of a 4 ft diameter manhole. However, rather than treating it element as a junction, you can model it as a storage node (detention pond). In that way, you define the area exactly.
Also, refer to the new StormNET User Manual. It describes junction entrance and exit loss coefficients more precisely. You can download it from this link:
ftp://ftp.bossintl.com/outgoing/Stor...ser_Manual.pdf