Cleric: Root - Calm - Atone (or atone stick) questions

[Izmael]

First, you don't necessarily need to root first. You can simply Calm and sneak past. Root is helpful if

1. You already have aggro on the mob and need to get rid of the aggro. Root will help as Calm and Atone can take a few casts to stick.
2. You have little trust in your Calming skillz and anticipate a possible crit fail (low CHA) and don't want to get smacked if and when it happens.

Now on to your questions.
"why use calm and not X". Until a recent patch, Calm was the best compromise between duration (once it sticks) and mana cost per attempt. I haven't played a relevant class in a long time but I understand that Pacify is now actually better, as it has been boosted in a recent patch.

"does he have to be at spawn point" : no, can work anywhere. Calm is there to prevent the mob from immediately reaggroing / reassisting after Atone sitcks. Root, as I said before, is an additional safety net in some situations, or if you already are getting whacked and need some breathing room.