Building churches or roofs that have a tower or another story going through can be a pain if you use the auto tools. I’m talking about something like this:
What you actually might be aiming for, though, is more something like this:
It can be done by covering part of your build that is going get a roof with slabs or floor. In this case, there are three different parts needed. Start with the two smaller ones. If you build the big one first and set up the two smaller ones, unnecessary parts will be generated clipping through each other. So you cover the large part put roof one and two up and set the slopes accordingly.
Then it’s time to erase the slabs from the bigger part and set up that roof as well. And that’s about it.
Only slight downside are the roof colors not being perfect. In my opinion it’s neglectable, though. Upside is, you can use differen view modes without a slab roof blocking the view.