By default all elements will belong to the story in which it's Base Height resides. And it doesn't matter if it is modeled in the 3D window or the Floor Plan window.
For example, if you have stories ground, first, and second, each with a height of 10' and your wall's base height (relative to Project Zero) is set to say anything greater than 10' and less than 20', it will appear in the first story.
But the confusion starts when we use the 'Show On/Link To Stories' setting (available for some elements), which by default this is set to Automatic. And you may want to check the explanation I posted
in this thread.
This setting only determines how the element will display in the floor plan window - it doesn't affect the base height of the element. In other words, if you are on the first story and go into the 3D window and model a wall that has a base height of 0 and is set to show on Current Story, it won't show on the first story. It will show on the story in which it's base height resides, which is the ground story. Keep in mind, according to the wall's settings, the base height is set relative to project zero, not the current story - take a look at the top of your Wall Settings dialog!
So why change this 'Show On/Link To Story' setting then? It becomes more important when we have multi-story walls. If you want to show a multi-story wall on every story it enters, then set it to Automatic. If not, set it to Current/Own Story Only.
My advice is this: When working in 3D, keep your eye on the element's base height. That will determine which story it shows on when you go back to the floor plan window. Leave your elements set to Automatic. If you go back to the floor plan window and see multi-story elements showing on unwanted stories, change them to show on Own Story only.
As Matthew mentioned, the Window's (vertical) Anchor can now be set relative to any story, as well as to the wall's base. Check under the Parameters panel of the Window Settings dialog. Same for doors and corner windows of course.
There are a lot of new settings in AC10, and most people get in trouble when they start playing with them!
Cheers,
Link.