The bit between the the existing room and the roof is called a frieze. It's been a while, but I think you have to type in a cheat to enable the frieze and then you build a foundation up there. Give me a few minutes and I'll open up my game and see if I can work it out. What house/neighbourhood is this?
**edit** To enable the placement of friezes, open the cheat console and type .... placefriezes on Then select the foundation and place it on top of the new section. To turn it off type placefriezes off
I'm not sure though why you can't place the roof because the frieze shouldn't stop it. I just did a quick test and could place a roof on the higher section with a frieze and the lower section next to it without the frieze. The chimney shouldn't stop it either. Do you get some sort of message when you try to place the roof? Something like can't intersect with other objects? That's the only thing I can think of, that there is something in the way.