I hope to not receive the default "We don't support multiple monitors" response. I have 3 22" monitors. When I launch Distant Worlds Universe the menu does not display to start a new game after the vanity videos and closing the Galactopedia. I have to disable two of my montiors before launching the game in order to be able to start a game.
I don't know how the 3 monitor setup actually works, but I never had an issue using it with my two monitors. Two as in my "new" and "old" one, not anything fancy :)
I doubt you can get the game to play on more than one monitor.
You can specify a window size by editing Startup.ini.