Manual Dormer Above Railing

[jarrex]

I have a dormer that needs to be above the stair railing, however when I manually create the wall, the railing cuts the roof siding wall in half which creates an odd hole in the roof:

 

 

 

The interior is fine

 

 

 

But I know it's the railing that's causing the issue because if I delete the wall that gets cut after the railing the hole disappears (but then the siding isn't filled in)

 

 

 

Any ideas as to how to fix this?