I have discussed the underlying issue here.
At the moment you can specify that the contents of a deck are face-up (“Never”), face-down (“Always”) or “via right-Click menu”. None of these quite fit the needs of Dominant Species.
I can definitely see ways of making the module comply with the game rules, but it won’t look exactly like a real game would. I can maybe see ways of improving the situation, but so far I have failed.
The natural solution would be that one could specify that the deck should be face-down but that the top card can be flipped to face-up (preferably via all the usual means: menu, hot-key etc.)