It is one layer of crisis per basic deck used. But, to be sincere, you can play 4 players with one basic deck and therefore one of each Crisis expansion. Just use the Scouts and Vipers of the second deck for the extra players but put the second deck and second Crisis away.
agree this is the best way to go. there are plenty of cards in one deck for a 4 player game. I just bought my second copy and crisis set, using the old starter cards and explorers from my first deck.