Glad you got it to clean up. May have just had to regenerate. The lower roof first is probably a good idea. May not always work best.
A lot with roofs has to do with how you use them. If you show framing and roof outlines and keep them as live drawings to use with construction documents it's one thing. If you want it just for elevations and 3D you can cut things up more without running into issues, then save as a 2D drawing and then work on that for your framing plans. It can be a whole different process of what to work at and what to let go of. If you don't need everything on one plan for roofs, sometimes breaking up and drawing first floor roofs on their floor and second floor roofs on their floor helps. Again, those stinking lollipops are needy and don't always behave. I know some folks use all sorts of adjustments to keep them out of the way (hidden beams, walls, etc.). Once you set your main pitch and get the heel heights you want, adjusting the others will automatically align eaves (if you set things right from the start).
I think they've made some improvements in 2022. I have yet to spend tons of time working on complicated projects as I wait the rooting out of the bugs. Will see how it does, but I suspect some of the things they claim to have worked on should help.