Again, you have to draw what you would expect to build ... You wouldn't build the roof off ceiling joists.
A bonus room would be EITHER built off a floor system, OR build with attic trusses.
If it's a floor, then you would have a single plate on it to fasten the roof joists to.
If it's an attic truss, then adjust the member thicknesses and heel heights in the roof parameters to suit.
Draw what you would build.
If you have issues with the roof attaching to the wrong walls, then temporarily adjust the plates (walls) so they are longer than the first floor walls and adjust the lollipops to suit, the adjust the walls back.