You need to make sure that there is water in the 2D area at the beginning of the run or else the 1D area will go dry. There are multiple ways of doing this, initial condition of the 2D area or hotstart.
Did you specify the reach lengths for the added XS? It is probably shown in plan view, but the reach length is set to zero and so it appears on top of another XS.
I generally do just this and set them all to the same. There are some cases where I then go back and adjust as needed, but that does not happen very often.
In the latest release of HEC-RAS 5.0, the 2D Vx and Vy values are not created by default (they were in the beta) and need to be turned on in the output options. Once this is turned on, the outputs will be in the hdf file.