shed roof clerestory and ceiling height

[ebdesign]

James,
Leave your walls at "default top/bottom" as much as possible. Control their hgt by defining your ceiling hgt in your rooms to the plate hgt you want it to build to. Use "lowered ceiling" for ceilings that are below the plate hgt. Select "balloon through ceiling" for the wall to build all the way to bottom of roof if that is what you want. Be sure that your roof framing is what you want.
I found some odd things in your plan. When I went into wall defaults to change the main layer of your SIPS wall, the front wall disappeared????? I discovered that when the siding always disappeared on the clerestory wall, even when there was no roof plane there. Other strange things that I hadn't seen before.
I drew the basic shell of your plan in a blank plan & didn't get this behavior.
Anyway, it's all in your room defs & wall properties.
HTH
Jim