Matthew, when you say "calculate culvert A", do you mean it calculates the HW for the combined flow it receives? I have been pulling my hair out over this for a few days now. I have a similar scenario where I am dealing with submerged weirs flowing into a "user" outlet pipe since hydraflow won't model my arch culverts. I cranked them out by hand/spreadsheet and determined their stage-discharge relationship.
So, for a given stage upstream of the multi-stage weir structures, "the HW produced by culvert A" (downstream of weir structures) will be the total flow rate from both contributing structures (Qr each) matched to the controlling HW depth for culvert A plugged into their Qs equation??
This doesn't seemed to be explained clearly in the user manual (or I am slow). I actually posted about this same issue recently.
Also, it would be nice for Hydraflow Express to allow modeling of combination weirs of the rectangle/v-notch variety.