Dear Brian :
When in doubt, run it mixed (both subcritical and supercritical).
However, if you are working in fairly flat areas, then keep it subcritical and check to see if in the HEC-RAS analysis results the computed water surface elevation is the same as the computed critical water surface elevation. For subcritical flow, the computed water surface elevation should always be above the critical water surface elevation. If not, then it is likely that there is supercritical flow at that cross-section (i.e., river station). Note, however, that you can model the stream as subcritical, and yet have supercritical flow within the culvert. This is a normal occurrence and you do not need to model the stream as supercritical in this case.
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