I think the limit on placing things is +/- 32000 x/y/z and that messes up havok ingame, but you can still actually place things there. Make sure your moving hte mouse enough, and snap to grid is off, then try. Also perhaps instead of having a door leading to stiars, linking to the cell. Link the door to the cell, then have the stairs down in the basemant cell.
I am trying to add a basemant to a two level interior because I basically "ran out of space." Because the interior I am working on needs to be scaled according to the size of the exterior, I can't just enlarge the room, which of course would be easier. My intent is to do something like what you described by adding a set of downward stairs from the first floor, then a door at the end of the stairs. But I want to simulate the impression that the basemant is located right benneath the first floor, rather than "branching out", if you know what I mean. I guess I can delete the navmesh and redo it. It's just a hassle I'd like to avoid.