My current practice to model an existing culvert includes digging a channel cutting through the existing embankment, then putting an internal connection which includes a culvert and embankment as an weir.
This practice is time consuming, and all of this complex task is just to avoid the software complains that the invert levels of the culvert is lower than the embankment cell, whilst in fact the existing culvert is lower than the cell representing the embankment
What is your practice?