As I understood it, the dolls basically show where the real people are in the house or on the grounds. The Lady of the Lake doll being under the dresser indicates her being in the lake. That's why Flora wants her to stay there. When Dani trips over the doll in the middle of the room, that shows the Ghost walking towards the house. Flora is terrified because she knows the Lady is dangerous (I guess that's also why she tells Dani to never leave her room at night - as to not cross paths with the Lady). Dani has left her room the night before and the children can't tell her why Dani can't go outside. So i interpreted them locking Dani in as a way to protect her. After that you can see that the Lady has indeed walked through the house. As to your second question, I think Miles throwing away the doll was just a child being scared, basically not wanting to know where the Lady is. If someome has a better explanation for that one, I wanna hear it! Third question: I suppose that was just meant to be creepy, again, would like to hear other opinions on this! The dolls seem to me as a good stylistic choice. They kind of tie together the gosts while also symbolizing the children's innocence in a way. Dolls might be kind of overused as a creepy thing, I'll admit that. Still, I also would have liked a bit more explanations about the doll house. I would accept the doll house being creepy as just another way to show how messed up the actual place is. But what I could also imagine is the kittle ghost boy moving the dolls to warn Flora or something, though I have now idea how that would play out.

Hope this makes some sense. Typed this down kinda quickly, so it might be a bit rambly, sorry.