I think you would be a lot more successful if you added depth to the floors on both of the levels and made them components. On the second floor, you would be able to punch through for the stairwell by going into the floor component(double clicking to edit it), drawing in the shape of the opening, then push/pull through and voila, the opening is there and the rest of the floor remains intact.
Add walls by drawing the lines onto the surface of the "closed" component floor and you can tweak them since they don't glue themselves to the floor like they do if the floor is not a component. By adding depth to the second story floor, you have an accurate total rise for the stairs if the depth corresponds to the thickness of the construction from the first floor ceiling to the actual floor on the second story.
Even though you don't "need" a super accurate drawing for what ever your purpose is, the more accurate you make it, and the better procedures used will make the over all job much easier.