If the cards are being underdecked from a known location it is the choice of the player carrying out the underdeck ability.
Examples--
Black/Gold Outsiders allows the controller of Outsiders to underdeck cards from play and that player gets to choose the order.
Persistent Pestering instructs the opponent to underdeck two good cards from his hand. Since it is the opponents choice, they get to choose the order.
If the cards are being underdecked after being revealed or looked at from the top of the deck, then they get underdecked in the same order in which they are revealed.
Examples would be: Lawless LS, Fishers of Men, Gideon's Call, Susanna and Mighty Warrior
However, some cards specifically allow the player to topdeck/underdeck a set of revealed cards in the order that they choose (Faith of Isaac, Divination & Balaam's Prophecy being a few examples).
