As solver says, absolutely learn the manual roof tools or else you would have to put all ceilings to their heights before the last roof change, keep auto roof turned off, build roof and then put that one lower ceiling room back to height needed. More work for each time plan changes, though.
I had this problem when I first used Home Designer. The easiest fix was to turn off auto roofs, build rooms with the same ceiling height (front living area same height as the back living area), build roof, keep auto roofs turned off and then change the height of the front living area to the height you need. I hope this helps you.