I assume you have left and right abutments and piers in each opening. If the openings are hydraulically “isolated” from each other, you may want to put each opening into separate parallel reaches that separate upstream of the openings and reconnect downstream of the openings. This will allow scour computations in each opening. Also note that if one or more openings scour more than the others, it may “capture” the other openings’ water and increase the Q in the favored openings, thus causing more scour than predicted by your method since it assumes a constant flow distribution into each opening for the flood event.