I'm not sure I get your problem, but if "blend in" means join = look as one piece, then I'd just stretch the upper roof as needed to cover the lower one's contour in plan. Then, if I want them to show on different floor plans, just cut it with the split tool and change the lower one's home story, making sure its level doesn't change (this requires AC11)
And place your AC version, platform and machine specs in your signature. please!
AC4.1-AC26SWE; MacOS13.5.1; MP5,1+MBP16,1