Setup (Dimensions Frame Dialog box) is an X value measured from somewhere (arbitrary) on the Seat tube relative to BB.
I do not know why the measurement starts there, And I cannot change the starting point
Also I cannot find the matching Y value in the Dimensions Dialog box
Seat tube Offset (total) in the Dimensions Frame Dialog box, does not show up in the drawing, when selected.
Although you say "Setup" I assume you mean setback. Setback is explained at: bikecad.ca/setback. I assume you are dealing with a sloping top tube frame and this is why the location of the dimension may seem arbitrary. However, as the above link explains, the measurement is aligned with the top tube head tube intersection. Normally, the Setback dimension is not coupled with a vertical component. However, if you wanted to know this as well, it would be BB to top tube - head tube junction (Vertical). You'll find that dimension in the Jig setup tab of the Dimensions dialog box.
Seat tube offset (total) is the total amount of offset in the seat tube due to the seat tube being offset in its attachment at the BB and due to any amount of bending in the seat tube. If the total offset is 0mm, then all you will see is a 0mm dimension oriented horizontally at the BB. I suspect this is what's happening in your case. If you believe you have some amount of offset and this dimension is not being shown, please send me your BCAD drawing and I will investigate.