Layout of the house

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I had the same questions about the layout, but one episode did show David going out the back kitchen door and then down some steps. You see his head through the window heading downward. So there's that. Some other episodes, however, seem to show some kind of back interior staircase going into the kitchen.
I had to try and remember my login to IMDB because I couldn't have your good question go without a reply.

The exterior and interior are not the same house.

Is you are that curious you can find and visit the house that they filmed at. I've seen it before.

I always saw it as the business part of the building was downstairs and the Fishers lived above. I think when Tracy is crying over her aunt in the Fishers sun room David tells Nate 'Tracy is upstairs' and Nate goes to find her and console her.

"Living our maggot lives, dreaming of becoming flies."

I'm currently trying to make a 3D model in Sketch Up becuase I live very close to the real residence.

The layout is NOT consistent to the outside.

For example, the stairs that lead up to the second floor near the door, are followed by the door way into the chapel. If you were at the landing where the bay window is situated before the stairs continue upward you would see the rest of the entrance room, the door to the chappel, and the end of the chappel where the stained glass window.

Lets say you were looking again with your back facing the second floor bay window in the real house, (where the landing is on the show)

the stained glass window (as seen in the chapel) would be perpendicular to that same bay window, not parallel to it. the chapel is also noticeably wider on the inside.