Dear Russ :
It is really your call. You can break the model down into a separate model for each structure, or model it as one continuous model. If you leave it as a single model, then adjust the discharge at locations along the river to account for the change in discharge.
If you have any additional questions or need any further information, please contact me again.
Sincerely,
Chris E. Maeder, M.S.
Senior Technical Engineer
chris.maeder@bossintl.com