Actually, HydroCAD will model a culvert with a reverse slope. Just enter a negative slope, or an outlet that is higher than the inlet. In addition to the normal culvert analysis, this will cause HydroCAD to consider weir-flow conditions at the outlet.
Note: This applies to a culvert outlet from a pond, not a pipe reach. Since a reach always operated under normal Mannings flow, it must have a positive slope.
As to your second questions, HydroCAD will allow an upstream node to be lower than a downstream node. This situation will generate a warning message to alert you to the tailwater condition, which can be handled by using the appropriate routing procedure and modeling approach. You can click the specific warning message for further details.