If you've got a yew tree in a graveyard outside an old stone church, chances are good your story's going to be set in the U.K, which is chock full of old cemeteries, yew trees, and things that go bump in the night. This kind of church and cemetery are more prevalent in England than they are in America. Take a look at this for an idea of what we're talking about. All cemeteries, all yew trees, all U.K., all the time.
There's an old saying, "Write what you know," and that's what Ness is doing here. He's an American expat in England, and chances are he's seen one or two (or seventeen) of these cemeteries. So why not put one behind Conor's house? After all, it's an easy way to work that yew tree into the story, with all its connotations of health, healing, and yes, death.
Smaller settings within the larger one include Conor's school and house, his grandmother's house, and his mother's hospital room. In every room, he (and the reader) is aware of the clocks; we need to know when the monster's going to show up. Everything's changing in Conor's life, right down to his dad's accent ("'Hey, son,' his dad said, his voice bending in that weird way that America had started to shape it" [12.37].)
That change is shown in constant contrasts, like the one between Conor's grandma's house and his own. He thinks the monster may not even come to visit there, because it can't: "Maybe it didn't know where his grandma lived. Or maybe it was just too far to come. She didn't have much of a yard anyway […] no room for a tree at all. It didn't even have grass" (12.2). One minute the monster's there, and one minute it's not, depending on Conor's location.