Emelie's plan from the start...
She accidentally smothered her child.
She covered this up.
She then moved to another state and city(said by her).
Scouted potential kids that would be her son's age now and kidnap the boy and brainwash him into thinking Emelie is his mother.
The youngest boy was the "Cubby".
And to clear things up that people seem confused about...
EMELIE HAD TWO ACCOMPLICES..
The start of the movie they pull up to Anna the babysitter and ask for directions...Emelie was in the backseat-Accomplice #1 was driving and Accomplice #2 ran up behind Anna and snatched her up.
..so..Emelie at the end of the movie has potential to get away if her other accomplice shows up eventually to give her a ride.