Hi
There are no good and bad way to define a port. You should choose one direction and phases of S parameters will be referenced to this direction. For an example, if you are analising multiport microstrip circuit use the same orientation for all ports, it doesn't matter if it is directed up or down as long as all of the ports have the same direction. If you chande the orientation of one port, the phases of transmission S parameters from this port to all other should change 180deg, the phase of reflection of this port should change 360deg=0deg.
Hope this helps
flyhigh