That is similar to low water crossings that I have done in the past and each would require hand or spreadsheet calculations. Unless you are using a modeling software that allows you to put in a table of areas and wetted perimeters. the only thing I have found was that the losses at the pipe...
I found that I could most easily use the excel formats or inmy case the openoffice.org software, or the staroffice products. In the spreadsheet I was able to import columns to the correct formats. This was using also the CSV format or comma delineation.