I'M just speculating what I think happened:
AGT was planning this - he had been watching Sierra. Knew that she was out early in the mornings. Somehow knew also that no one was around. He came that morning to take her. He drove his car down the cul-de-sac as she was leaving. Subdued her quickly by stunning or tazing her, Grabbed her phone while she was probably talking or texting on - listening to music on. Quickly put Sierra in the trunk of his car so no one could see her as he drove away. The bag was probably dropped and he picked it up and threw that in the trunk too or the car too.
Had her phone on him as he was driving away. Quickly threw the phone out on the side of the road.
Took Sierra wherever he was going to do his awful thing ( I shudder, don't even want to think about this part) Left her hidden (I don't think she was alive after this, sadly) While driving from where he left her realized he still had her bag in car. Knew he couldn't take it home, would raise the suspicions of his wife. Put the bag where he thought it would be well hidden, maybe to come back to to put somewhere more hidden later on.
Found out that LE was all over the case next day searching. At this point he could not go back to re-hide the bag. Clothes inside were neatly folded because he either did it (to make her look like a runaway) or Sierra had neatly folded them after he made her take them off, hoping to buy time. Perhaps there was urine on the clothes because when he tazed her she lost her bladder control. He had taken those same cloths off of her, and that's why his skin fragments are on the clothes. Perhaps Sierras DNA was found in trunk of his car. Perhaps he moved her twice, once after he killed her, and that's why LE says she is dead. They found evidence to show there was dead body in the trunk of the red Jetta.
Sierra is still where he left her, carefully hidden. He thought he had covered his tracks well and was not freaked about LE following him because he did not take into account DNA, there was no blood so he thought he could not be found. He did not take into account that were cameras all over MH that could spot his car. He thought he was home free.
He has done this before. Perhaps even killed before and got away with it. Feeling pretty cocky and self-assured and keeps telling his family "there is no evidence" after he knows he is being watched. That is why the family keeps parroting what he said. He felt there was no evidence to link him to his crime. Thank God for Codis and DNA. Should be in every state!
JMHO