Hi Haritha
In your scenario, a directional terminal configuration containing at least 2 downstream terminals should be set on the device connecting the pipes at the elevated manholes. One pipe would be assigned to one of the downstream terminals (ex. Outlet Port) and the other pipe would be assigned to the other downstream terminal (ex. Outlet Port 2).
I suggest not assigning the new directional terminal configuration to Pipe Connection > Pipe Connection (if this is the feature you are using to connect pipes at manholes). This will require you to set terminals at every manhole. Instead, create a new Pipe Connection asset type (ex. Elevated Manhole Connection) and assign the new directional terminal configuration to it.
Hope this helps and let me know if you have any additional questions.