Dear Rob :
The only way that you can model a custom shaped culvert is to either determine the rating curve for the culvert externally and then use that to define the head loss from the upstream cross section to the downstream cross section, or to model it as a bridge opening with the shape of your custom culvert.
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