I don't believe it matters. I just tore down and fully cleaned 3 vertical motors (2 from my FM Trainmaster and 1 from my Alco). In each case I closely observed the orientation of the thrust washers and no two motors were the same. That is no guarantee they were that way from original manufacture, since I bought them used 25 years ago.
But after reassembly, I decided to focus the "flat" sides toward the bushing. Been running them for weeks with no issue - but I would love some old timers to chime in and confirm.