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i am a bit confused. are you looking to model flow from the main channel flowing back upstream through the culvert? if so, i think you need to model as a lateral structure. if you are modeling flow in the positive flow direction down the channel, thru the culvert and into the river, you need at least 2 (maybe 3?) cross-sections downstream of the culvert BEFORE the junction to the mainchannel. if the culvert is submerged by the main channel, you made need to use a little imagination to create these cross-sections. if i have a correct picture of what you are doing, for these cross-sections, no matter what their shape, the model will flood them out anyway. i would just look at the results and see if they make sense. good luck.
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