I figured you populate the first room and then choose where your characters go. Seems to be part of the player choices and tactics. Randomly putting characters in there first leaves little decision making.
Also in other rooms, the monsters are revealed before characters have to decide where they will move to in there.
That makes the most sense -- I just couldn't find any source for this ruling, either in rules or in a post by Isaac. The only source I found was in an unofficial setup walkthrough.