You shouldn’t just add the peak flows unless they have coincident peaks. Usually the flow downstream of a confluence does not equal the sum of the trib and the main stream flow upstream of trib.
A lot of FEMA studies are done using peak regression flows or hydrographs that have been calibrated to regression flows as there is no other calibration data.
The answer about turning off junctions is, it is not possible. Once a junction is placed, you will need to specify reach names and junction inputs.