John - there is no reason that it should not work - there are 5 or 6 cases that the model uses for supercritical, subcritical, variations in tailwater & headwater, overflow, etc; however the model determines the case depending on your inputs. You may need to run it from both directions if you are not sure whether the culvert (or other channel up or downstream) is (are) all subcritical.
Good luck, Ron K
ronkilmartin@home.com