What Happens if I Manifest a Double-Faced Card?
This article explains that double-faced cards can be manifested and enter as 2/2's with no abilities.  The actual implementation of this stems from the fact that the double-faced card must already be unidentifiable in your hand and library.  As a result, you already have the card in an opaque sleeve or you have a checklist card in your deck as a placeholder, and either of these can be put on the battlefield face-down as a state distinct from transformed.

It should be noted that double-faced cards can't be turned face down if they are already a face up permanent (such as by Ixidron).  The relevant rules are the following:


  711.9. If an effect allows a player to cast a double-faced card as a face-down creature spell, or if a double-faced card enters the
  battlefield face down, it will have the characteristics given to it by
  the rule or effect that caused it to be face down. That card remains
  hidden, using either a face-down checklist card or opaque sleeves. See
  rule 707, “Face-Down Spells and Permanents.” 
  
  711.9a While face down, a double-faced permanent can’t transform. If it is turned face up, it will have its front face up.
  
  711.10. Double-faced permanents can’t be turned face down. If a spell or ability tries to turn a double-faced permanent face down, nothing
  happens.