In HydroCAD I would model the upgradient stream as a Reach with the appropriate inputs to model the stream characteristics, model the culvert as a second Reach with appropriate inputs to model the culvert characteristics, and then model the downgradient stream as a third Reach.
You'll have to make sure the Subcatchments feeding your stream are set up and connected to the Reaches to accurately model the entire watershed feeding into the stream (the subcatchments may be rather large if this is a perennial stream).
I'm not familiar with PondPack.
Hope this helps,
Derek