People have been asking about a stair calculator where the top tread is level with the upper floor, so:

http://www.blocklayer.com/stairs/stairs-toplevel.aspx

The top tread is level with the upper floor, so extends 1 run from it.
For notched stringers, with treads on top of the notches, the stringer joins to the upper floor flush with the top, so should be easier to attach.
Also for concrete stairs (check the 'Concrete Thick' check-box) it matches up to the upper floor better.

If it needs editing, adding to or fixing, please let me know.