Do 1st Floor Studs Always Align With 2nd Floor Studs

Floor joists align with the wall studs which align with the first story floor joists.
Do 1st floor studs always align with 2nd floor studs. I was thinking of building a 4 knee wall on the second floor then setting my rafters on that instead of directly on the floor like a true 1 1 2 story. 2 click the button in the edit toolbar to align the basement wall with the wall above. Aligning the first floor wall with the basement wall does not work. While first floor supports are needed to account for the additional weight of a second floor the walls are pretty much the same as those of a single story home.
The second floor studs did not stack over the floor joists below. Need to tie down 2nd floor studs to bond beam below 2nd floor wood trusses. I understand this is a problem as you are building the foundation first and doing this will move the foundation walls. The joists were offest by 6 8 from the studs.
But i ve been reading it might be better to extend my first floor studs the extra 4 instead. The walls will not automatically align themselves up. On a framing inspection i noticed 2 x 4 studs spaced at 16 oc for the first floor walls. Trusses bear on 2x plate with anchor bolts into masonry bond beam.
This will carry through to each subsequent story no matter how many. I have a two story structure first floor cmu 2nd story wood stud frame located in high wind area. The floor joists for the second floor did not stack directly above the studs. This will be in the northeast so snow load is a concern.
Any thoughts are appreciated.