Basically, the endings split when Telly goes into the warehouse alone and sees the "alien" for the first time. After she begins running after her son, the endings change. In the alternate ending, she chases her son and sees him in his room. The alien guy comes up and tells her stuff about the experiment. She tries to go to her kid but keeps getting knocked down by some force field. One shot of this is in the trailer, as she jumps across the "room" and it looks like lightning. She nearly kills herself doing this and the alien tells her she doesn't have to die, then the room and her son vanish and she is on the ground. He then tries to erase her memory but she holds out and he tells her something to the extent of "you are the only one who'll know." It then goes to the park from the main ending and she finds her kid, etc. The only diff. here is she that she goes to her son's room first and later sees the alien in the park walk away. This ending isn't as good imo, as the alien almost seems friendlier. In the theatrical, after she runs she goes all over, the alien pops up in a few jump scenes, breaks the glass, screams, etc. She sees visions of her son and he begins wiping them. This is basically the same as before but when she resists, aka remembers a memory of her pregnancy, the alien realizes she has won. He then says that he nees more time and is ripped into the sky.
Hope this ridiculously long explanation helps. I liked the theatrical better, because it kept a more menacing tone and was more suspenseful.