@mikes1987
I basically did the same thing you did, except that I made the part for the two levels a separate room first then removed the ceiling and floor. Fit the stairs in. Then raised the foundation by 1 full square up. I tried redoing the stairs, but from basement level, it only goes to ground level, not raised foundation level.
So to get the ground level top of the basement stairs to the raised foundation floor level, I had to make a 3 square room that matched grounds level, then put stairs there that goes from the basement stairs to the raised floor. After that I put walls back in and made a fence/gate.
https://i.imgur.com/l9yB3U6.jpg
It actually technically turns into 3 levels if you raise the foundation. Although you can directly connect stairs from the basement to the raised foundation level, you can't do that if you want an open ceiling-floor next to the stairs. Without making a second set of stairs.
https://i.imgur.com/kmkLuZg.png